Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells
Xue, L., Spahn, C.M.T., Schacherl, M., Mahamid, J.(2024) Nat Struct Mol Biol 
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Starting Models: experimental
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(2024) Nat Struct Mol Biol 
Entity ID: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S2 | E [auth A] | 294 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75560 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75560  Go to UniProtKB:  P75560 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75560 | ||||
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Entity ID: 6 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S3 | F [auth B] | 273 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P41205 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P41205  Go to UniProtKB:  P41205 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P41205 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S4 | G [auth C] | 205 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P46775 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P46775  Go to UniProtKB:  P46775 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P46775 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 8 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S5 | H [auth D] | 219 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q50301 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50301  Go to UniProtKB:  Q50301 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q50301 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 9 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S6 | I [auth E] | 215 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75543 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75543  Go to UniProtKB:  P75543 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75543 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 10 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S7 | J [auth F] | 155 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75545 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75545  Go to UniProtKB:  P75545 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75545 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 11 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S8 | K [auth G] | 142 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q50304 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50304  Go to UniProtKB:  Q50304 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q50304 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 12 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S9 | L [auth H] | 132 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75179 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75179  Go to UniProtKB:  P75179 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75179 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 13 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S10 | M [auth I] | 108 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75581 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75581  Go to UniProtKB:  P75581 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75581 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 14 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S11 | N [auth J] | 121 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q50296 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50296  Go to UniProtKB:  Q50296 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q50296 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 15 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S12 | O [auth K] | 139 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75546 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75546  Go to UniProtKB:  P75546 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75546 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 16 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S13 | P [auth L] | 124 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q50297 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50297  Go to UniProtKB:  Q50297 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q50297 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 17 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S14 type Z | Q [auth M] | 61 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q50305 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50305  Go to UniProtKB:  Q50305 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q50305 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 18 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S15 | R [auth N] | 86 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75173 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75173  Go to UniProtKB:  P75173 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75173 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 19 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S16 | S [auth O] | 94 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for A0A0H3DLS7 (Mycoplasmoides pneumoniae (strain ATCC 15531 / DSM 23978 / CIP 103766 / NBRC 14401 / NCTC 10119 / FH)) Explore A0A0H3DLS7  Go to UniProtKB:  A0A0H3DLS7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A0H3DLS7 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 20 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S17 | T [auth P] | 85 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q50309 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50309  Go to UniProtKB:  Q50309 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q50309 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 21 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S18 | U [auth Q] | 104 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75541 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75541  Go to UniProtKB:  P75541 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75541 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 22 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S19 | V [auth R] | 87 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75576 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75576  Go to UniProtKB:  P75576 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75576 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 23 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S20 | W [auth S] | 87 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P75237 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75237  Go to UniProtKB:  P75237 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75237 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 24 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
30S ribosomal protein S21 | X [auth T] | 60 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P57079 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P57079  Go to UniProtKB:  P57079 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P57079 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 26 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
50S ribosomal protein L31 | Z [auth x] | 97 | Mycoplasmoides pneumoniae M129 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P78020 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78020  Go to UniProtKB:  P78020 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P78020 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
23S ribosomal RNA | A [auth 3] | 2,907 | Mycoplasmoides pneumoniae M129 | ||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
16S ribosomal RNA | B [auth 5] | 1,520 | Mycoplasmoides pneumoniae M129 | ||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
tRNA-Asp (P-site) | C [auth 7] | 75 | Mycoplasmoides pneumoniae M129 | ||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
tRNA-Lys (A-site) | D [auth 8] | 76 | Mycoplasmoides pneumoniae M129 | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 25 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
mRNA | 21 | Mycoplasmoides pneumoniae M129 | |||
Sequence AnnotationsExpand | |||||
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Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SPD Query on SPD | AA [auth 5], DA [auth 5] | SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N | |||
N2P Query on N2P | CA [auth 5] | PENTANE-1,5-DIAMINE C5 H14 N2 VHRGRCVQAFMJIZ-UHFFFAOYSA-N | |||
PUT Query on PUT | BA [auth 5], EA [auth 5] | 1,4-DIAMINOBUTANE C4 H12 N2 KIDHWZJUCRJVML-UHFFFAOYSA-N | |||
ZN Query on ZN | CE [auth M], EE [auth Q] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
MG Query on MG | AB [auth 5] AC [auth 5] AD [auth 5] AE [auth K] BB [auth 5] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | Warp | 1.0.9 |
MODEL REFINEMENT | PHENIX | 1.20.1_4487 |
Funding Organization | Location | Grant Number |
---|---|---|
Chan Zuckerberg Initiative | United States | Visual Proteomics Imaging |
German Research Foundation (DFG) | Germany | -- |