4XDA
Vibrio cholerae O395 Ribokinase complexed with Ribose, ADP and Sodium ion.
- PDB DOI: https://doi.org/10.2210/pdb4XDA/pdb
- Classification: TRANSFERASE
- Organism(s): Vibrio cholerae O395
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2014-12-19 Released: 2015-03-04 
- Funding Organization(s): Department of Biotechnology, Department of Atomic Energy
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.225 
- R-Value Work: 0.186 
- R-Value Observed: 0.189 
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 |
Ribokinase | 309 | Vibrio cholerae O395 | Mutation(s): 0  Gene Names: rbsK, VC0395_0007, VC395_A0124 EC: 2.7.1.15 | ||
UniProt | |||||
Find proteins for A0A0H2UL04 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H2UL04  Go to UniProtKB:  A0A0H2UL04 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A0H2UL04 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ADP Query on ADP | F [auth A], H [auth B], I [auth B], L [auth C], O [auth D] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N | |||
RIB Query on RIB | E [auth A], K [auth C], N [auth D] | alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N | |||
NA Query on NA | G [auth A], J [auth B], M [auth C], P [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.225 
- R-Value Work: 0.186 
- R-Value Observed: 0.189 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 59.42 | α = 106.29 |
b = 70.7 | β = 97.65 |
c = 79.88 | γ = 98.68 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-03-04  Deposition Author(s): Paul, R., Patra, M.D., Sen, U.
Funding Organization | Location | Grant Number |
---|---|---|
Department of Biotechnology, Department of Atomic Energy | India | MSACR project |
Revision History (Full details and data files)
- Version 1.0: 2015-03-04
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary - Version 2.1: 2024-03-20
Changes: Data collection, Database references, Structure summary