2HOD
Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide
- PDB DOI:  https://doi.org/10.2210/pdb2HOD/pdb
- Classification: BLOOD CLOTTING/PEPTIDE
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2006-07-14 Released: 2007-05-29 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.347 
- R-Value Work: 0.268 
- R-Value Observed: 0.238 
This is version 2.0 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 | A, D, G, J | 87 | Homo sapiens | Mutation(s): 0  Gene Names: FGA | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02671 (Homo sapiens) Explore P02671  Go to UniProtKB:  P02671 | |||||
PHAROS:  P02671 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02671 | ||||
Protein Feature ViewExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrinogen beta chain | B, E, H, K | 328 | Homo sapiens | Mutation(s): 0  Gene Names: FGB | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675 | |||||
PHAROS:  P02675 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02675 | ||||
Protein Feature ViewExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fibrinogen, gamma polypeptide | C, F, I, L | 323 | Homo sapiens | Mutation(s): 0  Gene Names: FGG, PRO2061 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679 | |||||
PHAROS:  P02679 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02679 | ||||
Protein Feature ViewExpand | |||||
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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 | Ligand Interaction | ||
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 | Ligand Interaction |
Modified Residues  1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
HYP Query on HYP | M, N, O, P, Q, R, S, T | L-PEPTIDE LINKING | C5 H9 N O3 | PRO |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.347 
- R-Value Work: 0.268 
- R-Value Observed: 0.238 
- Space Group: P 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 81.647 | α = 90 |
b = 47.069 | β = 90.06 |
c = 431.46 | γ = 90 |
Software Name | Purpose |
---|---|
AMoRE | phasing |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
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: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, 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