1I9C

GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENOSYLCOBALAMIN AND SUBSTRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase

Gruber, K.Reitzer, R.Kratky, C.

(2001) Angew Chem Int Ed Engl 40: 3377-3380


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMATE MUTASE
A, C
137Clostridium cochleariumMutation(s): 0 
Gene Names: GLMS
EC: 5.4.99.1
UniProt
Find proteins for P80078 (Clostridium cochlearium)
Explore P80078 
Go to UniProtKB:  P80078
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80078
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMATE MUTASE
B, D
483Clostridium cochleariumMutation(s): 0 
Gene Names: GLME
EC: 5.4.99.1
UniProt
Find proteins for P80077 (Clostridium cochlearium)
Explore P80077 
Go to UniProtKB:  P80077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80077
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
5AD
Query on 5AD

Download Ideal Coordinates CCD File 
F [auth B],
J [auth D]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
2AS
Query on 2AS

Download Ideal Coordinates CCD File 
H [auth B],
L [auth D]
(2S,3S)-3-methyl-aspartic acid
C5 H9 N O4
LXRUAYBIUSUULX-HRFVKAFMSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
G [auth B],
K [auth D]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.348α = 90
b = 113.139β = 96
c = 108.439γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2012-10-24
    Changes: Non-polymer description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description