2GC4

Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.

Structural Biology Knowledgebase: 2GC4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.173

Literature

Macromolecules
Sequence Display for 2GC4

Classification: Oxidoreductase Electron transport

Total Structure Weight: 340575.00

Macromolecule Entities
Molecule Chains Length Organism Details
Methylamine dehydrogenase heavy chain A, E, I, M 386 Paracoccus denitrificans EC#: 1.4.9.1 IUBMB
Gene Name(s): mauB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Methylamine dehydrogenase light chain B, F, J, N 131 Paracoccus denitrificans EC#: 1.4.9.1 IUBMB
Mutation: W57X
Gene Name(s): mauA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Amicyanin C, G, K, O 105 Paracoccus denitrificans Gene Name(s): mauC ami
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c-L D, H, L, P 147 Paracoccus denitrificans Gene Name(s): moxG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

D, H, L, P PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

C, G, K, O COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

D, H, L, P SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TRQ
Query on TRQ
B, F, J, N L-PEPTIDE LINKING C11 H10 N2 O4 TRP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.173
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.37 α = 90.00
b = 188.98 β = 99.74
c = 128.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-13
  • Released Date: 2006-11-28
  • Deposition author(s): Chen, Z., Durley, R., Davidson, V.L., Mathews, F.S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4