1N86
Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and GHRPLDK peptide ligands.
- PDB DOI: https://doi.org/10.2210/pdb1N86/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2002-11-19 Released: 2003-01-07 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.289 
- R-Value Work: 0.226 
- R-Value Observed: 0.230 
wwPDB Validation   3D Report Full Report
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 |
Fibrin alpha/alpha-E 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 | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrin 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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrin gamma chain | 324 | 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
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
fibrin alpha chain peptide ligand fragment Gly-Pro-Arg | 3 | N/A | 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   | |||||
UniProt Group | P02671 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by: Sequence | 3D Structure
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
fibrin beta chain peptide ligand fragment Gly-His-Arg-Pro-Leu-Asp-Lys | 7 | N/A | 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   | |||||
UniProt Group | P02675 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NDG Query on NDG | K [auth B], O [auth E], R [auth I], S [auth J] | 2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N | |||
MAN Query on MAN | L [auth B] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N | |||
CA Query on CA | M [auth B], N [auth C], P [auth E], Q [auth F] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.289 
- R-Value Work: 0.226 
- R-Value Observed: 0.230 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 52.328 | α = 90 |
b = 130.093 | β = 90 |
c = 298.313 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
CNS | refinement |
Entry History 
Deposition Data
- Released Date: 2003-01-07  Deposition Author(s): Yang, Z., Pandi, L., Doolittle, R.F.
Revision History (Full details and data files)
- Version 1.0: 2003-01-07
Type: Initial release - Version 1.1: 2008-04-28
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary