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 
• Deposition Author(s): Yang, Z., Pandi, L., Doolittle, R.F.

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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 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A4B2C1D1E1F1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 172.8 kDa 
• Atom Count: 11,054 
• Modelled Residue Count: 1,366 
• Deposited Residue Count: 1,498 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrin alpha/alpha-E chain	A, D	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrin beta chain	B, E	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrin gamma chain	C, F	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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
fibrin alpha chain peptide ligand fragment Gly-Pro-Arg	G, H	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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
fibrin beta chain peptide ligand fragment Gly-His-Arg-Pro-Leu-Asp-Lys	I, J	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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	L [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
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 Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-07 
Deposition Author(s): Yang, Z., Pandi, L., Doolittle, R.F.

Revision History  

• 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