4MY9

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor C91


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor C91

Kim, Y.Makowska-Grzyska, M.Gu, M.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
384Bacillus anthracis str. AmesMutation(s): 0 
Gene Names: guaBBA_0008BAS0011GBAA_0008
EC: 1.1.1.205
UniProt
Find proteins for A0A6L8P2U9 (Bacillus anthracis)
Explore A0A6L8P2U9 
Go to UniProtKB:  A0A6L8P2U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6L8P2U9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C91
Query on C91

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
FA [auth H]
J [auth A]
M [auth B]
AA [auth F],
CA [auth G],
FA [auth H],
J [auth A],
M [auth B],
Q [auth C],
U [auth D],
X [auth E]
N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide
C24 H18 N4 O
XYCMWFINXXFAFG-UHFFFAOYSA-N
IMP
Query on IMP

Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
I [auth A]
L [auth B]
P [auth C]
BA [auth G],
EA [auth H],
I [auth A],
L [auth B],
P [auth C],
T [auth D],
W [auth E],
Z [auth F]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
DA [auth G]
GA [auth H]
K [auth A]
N [auth B]
O [auth B]
DA [auth G],
GA [auth H],
K [auth A],
N [auth B],
O [auth B],
R [auth C],
S [auth C],
V [auth D],
Y [auth E]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
C91 BindingDB:  4MY9 Ki: min: 44, max: 820 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/m34my9
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.93α = 98.7
b = 89.883β = 90.32
c = 104.621γ = 96.46
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: 2014-06-11
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references, Structure summary
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description