2HLO
Crystal Structure of Fragment D-dimer from Human Fibrin Complexed with Gly-hydroxyPro-Arg-Pro-amide
- DOI: 10.2210/pdb2HLO/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2006-07-08 Released: 2007-07-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.268 
- R-Value Work: 0.210 
- R-Value Observed: 0.202 
wwPDB Validation   3D Report Full Report

Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrin alpha chain | A, D | 87 | Homo sapiens | Mutation(s): 0  Gene Names: FGA | ![]() |
Find proteins for P02671 (Homo sapiens) Explore P02671  Go to UniProtKB:  P02671 | |||||
NIH Common Fund Data Resources | |||||
PHAROS:  P02671 GTEx:  ENSG00000171560 | |||||
Protein Feature ViewExpand | |||||
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Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrin beta chain | B, E | 328 | Homo sapiens | Mutation(s): 0  Gene Names: FGB | ![]() |
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675 | |||||
NIH Common Fund Data Resources | |||||
PHAROS:  P02675 GTEx:  ENSG00000171564 | |||||
Protein Feature ViewExpand | |||||
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Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrin, gamma polypeptide | C, F | 324 | Homo sapiens | Mutation(s): 0  Gene Names: FGG, PRO2061 | ![]() |
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679 | |||||
NIH Common Fund Data Resources | |||||
PHAROS:  P02679 GTEx:  ENSG00000171557 | |||||
Protein Feature ViewExpand | |||||
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Oligosaccharides
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | I | 2 | | N-Glycosylation | Oligosaccharides Interaction |
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | J | 2 | | N-Glycosylation | Oligosaccharides Interaction |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CA Query on CA | B, C, E, F | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | Ligand Interaction |
Modified Residues  1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
HYP Query on HYP | G,H | L-PEPTIDE LINKING | C5 H9 N O3 | PRO |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.268 
- R-Value Work: 0.210 
- R-Value Observed: 0.202 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 54.69 | α = 90 |
b = 149.48 | β = 90 |
c = 232.93 | γ = 90 |
Software Name | Purpose |
---|---|
ADSC | data collection |
AMoRE | phasing |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Deposited Date: 2006-07-08 
- Released Date: 2007-07-17  Deposition Author(s): Doolittle, R.F., Kollman, J.M., Chen, A., Pandi, L.
Revision History 
- Version 1.0: 2007-07-17
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: Atomic model, Data collection, Derived calculations, Structure summary