2HPC

Crystal structure of fragment D from Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-amide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen alpha chain
A, D, G, J
87Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02671 (Homo sapiens)
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Go to UniProtKB:  P02671
PHAROS:  P02671
GTEx:  ENSG00000171560 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02671
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen beta chain
B, E, H, K
328Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P02675
GTEx:  ENSG00000171564 
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UniProt GroupP02675
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen, gamma polypeptide
C, F, I, L
323Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens)
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Go to UniProtKB:  P02679
PHAROS:  P02679
GTEx:  ENSG00000171557 
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UniProt GroupP02679
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gly-Pro-Arg-Pro-amide peptide ligand
M, N, O, P, Q
M, N, O, P, Q, R, S, T
5N/AMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth H],
EA [auth K],
U [auth B],
X [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth H]
DA [auth I]
FA [auth K]
GA [auth K]
AA [auth F],
CA [auth H],
DA [auth I],
FA [auth K],
GA [auth K],
HA [auth L],
V [auth B],
W [auth C],
Y [auth E],
Z [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.279 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.677α = 90
b = 46.069β = 89.99
c = 429.901γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary