8I7H

Meso-Diaminopimelate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Analysis of the catalytic mechanism of meso-DAPDH and extension of D-aromatic amino acid substrate scope

Wu, T.F.Song, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meso-diaminopimelate D-dehydrogenase
A, B, C, D
299Proteus vulgarisMutation(s): 0 
Gene Names: EKQ45_05540
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
API (Subject of Investigation/LOI)
Query on API

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
P [auth C]
E [auth A],
F [auth A],
K [auth B],
L [auth B],
P [auth C],
Q [auth C],
U [auth D],
V [auth D]
2,6-DIAMINOPIMELIC ACID
C7 H14 N2 O4
GMKMEZVLHJARHF-SYDPRGILSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
AA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
R [auth C],
S [auth C],
T [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.3α = 90
b = 213.3β = 90
c = 245.84γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release