4O03
Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167
- PDB DOI: https://doi.org/10.2210/pdb4O03/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Cricetinae
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 2013-12-13 Released: 2014-05-21 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.38 Å
- R-Value Free: 0.279 
- R-Value Work: 0.233 
- R-Value Observed: 0.235 
This is version 1.5 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 |
Prothrombin | 557 | Homo sapiens | Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5 Membrane Entity: Yes  | ||
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 | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A], H [auth A], I [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CA Query on CA | B [auth A], C [auth A], D [auth A], E [auth A], F [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
CGU Query on CGU | A | L-PEPTIDE LINKING | C6 H9 N O6 | GLU |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.38 Å
- R-Value Free: 0.279 
- R-Value Work: 0.233 
- R-Value Observed: 0.235 
- Space Group: C 1 2 1
- Diffraction Data: https://doi.org/10.15785/SBGRID/70
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 177.459 | α = 90 |
b = 89.431 | β = 116.36 |
c = 87.982 | γ = 90 |
Software Name | Purpose |
---|---|
CrystalClear | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-05-21  Deposition Author(s): Pozzi, N., Chen, Z., Shropshire, D.B., Pelc, L.A., Di Cera, E.
Revision History (Full details and data files)
- Version 1.0: 2014-05-21
Type: Initial release - Version 1.1: 2014-06-25
Changes: Database references - Version 1.2: 2017-08-23
Changes: Refinement description, Source and taxonomy - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary - Version 1.5: 2023-12-06
Changes: Data collection