5EDM
Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I )
- PDB DOI: https://doi.org/10.2210/pdb5EDM/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Mesocricetus auratus
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 2015-10-21 Released: 2016-01-20 
- Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.236 
- R-Value Work: 0.196 
- R-Value Observed: 0.198 
This is version 2.2 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 | 568 | 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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Oligosaccharides
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | J [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | S [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
MG Query on MG | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.20 Å
- R-Value Free: 0.236 
- R-Value Work: 0.196 
- R-Value Observed: 0.198 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 109.884 | α = 90 |
b = 168.69 | β = 90 |
c = 144.315 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-01-20  Deposition Author(s): Pozzi, N., Chen, Z., Di Cera, E.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) | United States | HL049413, HL073813 and HL112303 (EDC) |
Revision History (Full details and data files)
- Version 1.0: 2016-01-20
Type: Initial release - Version 1.1: 2016-01-27
Changes: Database references - Version 1.2: 2016-03-30
Changes: Database references - Version 1.3: 2017-08-09
Changes: Database references, Derived calculations - Version 1.4: 2017-09-06
Changes: Author supporting evidence - Version 1.5: 2019-12-04
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary - Version 2.2: 2023-11-15
Changes: Data collection