2HPC
Crystal structure of fragment D from Human Fibrinogen Complexed with Gly-Pro-Arg-Pro-amide.
- PDB DOI: https://doi.org/10.2210/pdb2HPC/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2006-07-17 Released: 2007-05-29 
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 
Starting Model: experimental
View more details
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrinogen alpha chain | 87 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02671 (Homo sapiens) Explore P02671  Go to UniProtKB:  P02671 | |||||
PHAROS:  P02671 GTEx:  ENSG00000171560  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02671 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrinogen beta chain | 328 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675 | |||||
PHAROS:  P02675 GTEx:  ENSG00000171564  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02675 | ||||
Glycosylation | |||||
Glycosylation Sites: 1 | Go to GlyGen: P02675-1 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrinogen, gamma polypeptide | 323 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679 | |||||
PHAROS:  P02679 GTEx:  ENSG00000171557  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02679 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by: Sequence | 3D Structure
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | 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 | AA [auth F] CA [auth H] DA [auth I] FA [auth K] GA [auth K] | 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 = 81.677 | α = 90 |
b = 46.069 | β = 89.99 |
c = 429.901 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2007-05-29  Deposition Author(s): Doolittle, R.F., Kollman, J.M., Chen, A., Pandi, L.
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