6LYL

Crystal structure of S1052D mutant of Formylglycinamidine synthetase

PDB DOI: https://doi.org/10.2210/pdb6LYL/pdb

Classification: LIGASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-02-14 Released: 2021-02-17
Deposition Author(s): Sharma, N., Tanwar, A.S., Anand, R.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.192
R-Value Work: 0.153
R-Value Observed: 0.155

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase.

Sharma, N., Singh, S., Tanwar, A.S., Mondal, J., Anand, R.

(2022) ACS Catal 12: 1930-1944

DOI: https://doi.org/10.1021/acscatal.1c05521

Macromolecule Content

Total Structure Weight: 146.33 kDa
Atom Count: 10,987
Modelled Residue Count: 1,288
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine synthase	A	1,304	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 1 Gene Names: purL, STM2565 EC: 6.3.5.3
UniProt
Find proteins for P74881 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P74881 Go to UniProtKB: P74881
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P74881
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth A] SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain Y [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] J [auth A] B [auth A], C [auth A], D [auth A], E [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain IA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain IA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain IA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain LA [auth A] SDF format, chain MA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A]	LA [auth A], MA [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain LA [auth A] Focus chain MA [auth A] Interactions & Density Focus chain LA [auth A] Focus chain MA [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]