2XWB

Crystal Structure of Complement C3b in complex with Factors B and D

Structural Biology Knowledgebase: 2XWB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XWB

Classification: HYDROLASE

Total Structure Weight: 566825.31

Macromolecule Entities
Molecule Chains Length Organism Details
COMPLEMENT C3B BETA CHAIN A, C 642 Homo sapiens Fragment: RESIDUES 23-664
Gene Name(s): C3 Gene View CPAMD1
COMPLEMENT C3B ALPHA' CHAIN B, D 912 Homo sapiens Fragment: RESIDUES 752-1663
Mutation: Q991E
Gene Name(s): C3 Gene View CPAMD1
COMPLEMENT FACTOR B F, H 732 Homo sapiens EC#: 3.4.21.47 IUBMB
Fragment: RESIDUES 35-764
Mutation: D254G, N260D
Gene Name(s): CFB Gene View BF BFD
COMPLEMENT FACTOR D I, J 228 Homo sapiens EC#: 3.4.21.46 IUBMB
Mutation: S183A
Gene Name(s): CFD Gene View DF PFD

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

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

F, H BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

I, J GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C, F, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.189
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 108.28 α = 95.47
b = 135.77 β = 110.69
c = 149.98 γ = 113.39

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-11-01
  • Released Date: 2011-01-12
  • Deposition author(s): Forneris, F., Ricklin, D., Wu, J., Tzekou, A., Wallace, R.S., Lambris, J.D., Gros, P.

Revision History

  • 2012-04-11
    Type: Citation | Details: JRNL
  • 2012-04-11
    Type: Non-polymer description | Details: HETSYN
  • 2012-04-11
    Type: Other | Details: CRYST1,REMARK 900
  • 2012-04-11
    Type: Version format compliance | Details: REMARK 4