1KDG

Crystal structure of the flavin domain of cellobiose dehydrogenase

Structural Biology Knowledgebase: 1KDG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.169
  • R-Value Work: 0.133

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KDG

Classification: oxidoreductase

Total Structure Weight: 121620.33

Macromolecule Entities
Molecule Chains Length Organism Details
cellobiose dehydrogenase A, B 546 Phanerochaete chrysosporium EC#: 1.1.99.18 IUBMB
Fragment: C-terminal flavoprotein domain
Gene Name(s): CDH-1 CDH-2

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6FA
Query on 6FA

A, B 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O16 P2
BJSUUWFQAMLNKU-OKXKTURISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EMT
Query on EMT

A 2-(ETHYLMERCURI-THIO)-BENZOIC ACID
C9 H10 Hg O2 S
HXQVQGWHFRNKMS-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HG
Query on HG

A, B MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

B UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.169
  • R-Value Work: 0.133
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 185.07 α = 90.00
b = 185.07 β = 90.00
c = 81.03 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-13
  • Released Date: 2002-11-13
  • Deposition author(s): Hallberg, B.M., Henriksson, G., Pettersson, G., Divne, C.

Revision History

  • 2012-05-09
    Type: Function and keywords | Details: changed E.C. number
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4