1LWU

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide

Structural Biology Knowledgebase: 1LWU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.245

Literature

Macromolecules
Sequence Display for 1LWU

Classification: BLOOD CLOTTING

Total Structure Weight: 363016.75

Macromolecule Entities
Molecule Chains Length Organism Details
Fibrinogen alpha-1 chain A, D, G, J 119 Petromyzon marinus Fragment: fragment
Mutation: T153A
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fibrinogen beta chain B, E, H, K 323 Petromyzon marinus Fragment: Segment 2 of 2
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fibrinogen gamma chain C, F, I, L 323 Petromyzon marinus Mutation: S137P
Gene Name(s): FGG Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ligand Gly-His-Arg-Pro-NH2 M, N, O, P 5 synthetic

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDG
Query on NDG

B, D, H, K, M, N, O 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

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

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

H BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

B, C, F, H, J, L, N, P ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-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)
NH2
Query on NH2

M, N, O, P AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYAF
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
NH2
Query on NH2
M, N, O, P NON-POLYMER H2 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.245
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 76.74 α = 88.81
b = 47.65 β = 97.23
c = 244.65 γ = 86.17

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-03
  • Released Date: 2002-08-23
  • Deposition author(s): Yang, Z., Spraggon, G., Pandi, L., Everse, S.J., Riley, M., Doolittle, R.F.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update