2HOD

Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.347
  • R-Value Work: 0.268

Literature

Macromolecules
Sequence Display for 2HOD

Classification: BLOOD CLOTTING / PEPTIDE

Total Structure Weight: 342815.69

Macromolecule Entities
Molecule Chains Length Organism Details
Fibrinogen alpha chain A, D, G, J 87 Homo sapiens Gene Name(s): FGA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fibrinogen beta chain B, E, H, K 328 Homo sapiens Gene Name(s): FGB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fibrinogen, gamma polypeptide C, F, I, L 323 Homo sapiens Gene Name(s): FGG Gene View PRO2061
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Gly-hydroxyPro-Arg-Pro-amide peptide ligand M, N, O..., P, Q, R, S, TM, N, O, P, Q, R, S, T 5 synthetic

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

E 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

B, H, K N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B, C, E, F, H, I, K, L CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
HYP
Query on HYP
M, N, O, P, Q, R, S, T L-PEPTIDE LINKING C5 H9 N O3 PRO
NH2
Query on NH2
M, N, O, P, Q, R, S, T NON-POLYMER H2 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.347
  • R-Value Work: 0.268
  • Space Group: P 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 81.65 α = 90.00
b = 47.07 β = 90.06
c = 431.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-07-14
  • Released Date: 2007-05-29
  • Deposition author(s): Doolittle, R.F., Kollman, J.M., Chen, A., Pandi, L.

Revision History

  • Version 1_0: 2007-05-29

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance