4Q33

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
363Clostridium perfringens ATCC 13124Mutation(s): 0 
Gene Names: CPF_2558guaB
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2YRZ7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2YA
Query on 2YA

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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
IMP
Query on IMP

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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
SO4
Query on SO4

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U [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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BA [auth F],
Y [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY
Query on ACY

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Q [auth D]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
FMT
Query on FMT

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/m34q33
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.121α = 70.82
b = 89.247β = 72.66
c = 99.185γ = 79.3
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

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