4Q33

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and A110

PDB DOI: https://doi.org/10.2210/pdb4Q33/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium perfringens ATCC 13124
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-04-10 Released: 2014-07-09
Deposition Author(s): Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Gu, M., Zhang, M., Mandapati, K., Gollapalli, D.R., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.243 (Depositor), 0.240 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

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

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and A110

Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Gu, M., Zhang, M., Mandapati, K., Gollapalli, D.R., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 313.91 kDa
Atom Count: 20,930
Modelled Residue Count: 2,746
Deposited Residue Count: 2,904
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	363	Clostridium perfringens ATCC 13124	Mutation(s): 0 Gene Names: CPF_2558, guaB EC: 1.1.1.205
UniProt
Find proteins for A0A0H2YRZ7 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YRZ7 Go to UniProtKB: A0A0H2YRZ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2YRZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2YA Query on 2YA Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain GA [auth H] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain S [auth E] SDF format, chain W [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth E] MOL2 format, chain W [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth E] mmCIF format, chain W [auth F]	DA [auth G] GA [auth H] J [auth A] L [auth B] M [auth B] DA [auth G], GA [auth H], J [auth A], L [auth B], M [auth B], O [auth C], S [auth E], W [auth F]	4-[(1R)-1-[1-(4-chlorophenyl)-1,2,3-triazol-4-yl]ethoxy]-1-oxidanyl-quinoline C₁₉ H₁₅ Cl N₄ O₂ SVKHERCOWKMPQO-CYBMUJFWSA-N		Interactions Focus chain DA [auth G] Focus chain GA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain S [auth E] Focus chain W [auth F] Interactions & Density Focus chain DA [auth G] Focus chain GA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain S [auth E] Focus chain W [auth F]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain V [auth F] SDF format, chain FA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain V [auth F] MOL2 format, chain FA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain V [auth F] mmCIF format, chain FA [auth H]	CA [auth G] FA [auth H] I [auth A] K [auth B] N [auth C] CA [auth G], FA [auth H], I [auth A], K [auth B], N [auth C], P [auth D], R [auth E], V [auth F]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain V [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain V [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain U [auth E] MOL2 format, chain U [auth E] mmCIF format, chain U [auth E]	U [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain U [auth E] Interactions & Density Focus chain U [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain Y [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain Y [auth F]	BA [auth F], Y [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth F] Focus chain Y [auth F]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain IA [auth H] SDF format, chain T [auth E] SDF format, chain X [auth F] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain T [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain T [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth F]	AA [auth F] EA [auth G] HA [auth H] IA [auth H] T [auth E] AA [auth F], EA [auth G], HA [auth H], IA [auth H], T [auth E], X [auth F], Z [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain T [auth E] Focus chain X [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain T [auth E] Focus chain X [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.243 (Depositor), 0.240 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34q33

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.121	α = 70.82
b = 89.247	β = 72.66
c = 99.185	γ = 79.3

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2017-07-26
Changes: Refinement description, Source and taxonomy
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description