4BDV
CRYSTAL STRUCTURE OF A TRUNCATED B-DOMAIN HUMAN FACTOR VIII
- PDB DOI: https://doi.org/10.2210/pdb4BDV/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2012-10-08 Released: 2013-05-15 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.98 Å
- R-Value Free: 0.246 
- R-Value Work: 0.162 
- R-Value Observed: 0.166 
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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
FACTOR VIIIA HEAVY CHAIN, 92 KDA ISOFORM, B DOMAIN | 760 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00451 (Homo sapiens) Explore P00451  Go to UniProtKB:  P00451 | |||||
PHAROS:  P00451 GTEx:  ENSG00000185010  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00451 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
FACTOR VIIIA LIGHT CHAIN | 685 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00451 (Homo sapiens) Explore P00451  Go to UniProtKB:  P00451 | |||||
PHAROS:  P00451 GTEx:  ENSG00000185010  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00451 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G89225LT GlyCosmos:  G89225LT GlyGen:  G89225LT |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ZN Query on ZN | E [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CU1 Query on CU1 | H [auth B] | COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N | |||
EDO Query on EDO | G [auth A], I [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
CA Query on CA | F [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.98 Å
- R-Value Free: 0.246 
- R-Value Work: 0.162 
- R-Value Observed: 0.166 
- Space Group: P 41 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 133.84 | α = 90 |
b = 133.84 | β = 90 |
c = 355.81 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | phasing |
Entry History 
Deposition Data
- Released Date: 2013-05-15  Deposition Author(s): Svensson, L.A., Thim, L., Olsen, O.H., Nicolaisen, E.M.
Revision History (Full details and data files)
- Version 1.0: 2013-05-15
Type: Initial release - Version 1.1: 2017-01-25
Changes: Data collection - Version 1.2: 2018-01-17
Changes: Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary