3P70
Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction
- PDB DOI: https://doi.org/10.2210/pdb3P70/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2010-10-11 Released: 2011-09-28 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.279 
- R-Value Work: 0.207 
- R-Value Observed: 0.210 
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 |
HUMAN ALPHA-THROMBIN, LIGHT CHAIN | 36 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.5 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HUMAN ALPHA-THROMBIN, HEAVY CHAIN | 259 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.5 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HUMAN FACTOR V, A2-B DOMAIN LINKER | I [auth M], J [auth N], K [auth O], L [auth P] | 71 | Homo sapiens | Mutation(s): 0  Gene Names: F5 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P12259 (Homo sapiens) Explore P12259  Go to UniProtKB:  P12259 | |||||
PHAROS:  P12259 GTEx:  ENSG00000198734  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P12259 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | O [auth B], U [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
BGC Query on BGC | DA [auth H], S [auth B], Z [auth F] | beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N | |||
BEN Query on BEN | BA [auth H], P [auth B], V [auth D], X [auth F] | BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N | |||
NA Query on NA | AA [auth G] CA [auth H] Q [auth B] R [auth B] T [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.279 
- R-Value Work: 0.207 
- R-Value Observed: 0.210 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 62.243 | α = 72.57 |
b = 68.227 | β = 84.05 |
c = 98.972 | γ = 80.45 |
Software Name | Purpose |
---|---|
MxCuBE | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2011-09-28  Deposition Author(s): Corral-Rodriguez, M.A., Bock, P.E., Hernandez-Carvajal, E., Gutierrez-Gallego, R., Fuentes-Prior, P.
Revision History (Full details and data files)
- Version 1.0: 2011-09-28
Type: Initial release - Version 1.1: 2012-02-29
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary