5GHF | pdb_00005ghf

Transaminase with L-ala

PDB DOI: https://doi.org/10.2210/pdb5GHF/pdb

Classification: TRANSFERASE
Organism(s): Brucella anthropi ATCC 49188
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-19 Released: 2017-05-24
Deposition Author(s): Kim, J., Park, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.174 (Depositor), 0.180 (DCC)
R-Value Work:
0.135 (Depositor), 0.150 (DCC)
R-Value Observed:
0.137 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Active Site Engineering of omega-Transaminase Guided by Docking Orientation Analysis and Virtual Activity Screening

Han, S.-W., Kim, J., Cho, H.-S., Shin, J.-S.

(2017) ACS Catal 7: 3752-3762

DOI: https://doi.org/10.1021/acscatal.6b03242

Macromolecule Content

Total Structure Weight: 99.91 kDa
Atom Count: 7,526
Modeled Residue Count: 855
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class-III	A, B	456	Brucella anthropi ATCC 49188	Mutation(s): 0 Gene Names: Oant_0199
UniProt
Find proteins for A6WVC6 (Brucella anthropi (strain ATCC 49188 / DSM 6882 / CCUG 24695 / JCM 21032 / LMG 3331 / NBRC 15819 / NCTC 12168 / Alc 37)) Explore A6WVC6 Go to UniProtKB: A6WVC6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6WVC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMP Query on PMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.174 (Depositor), 0.180 (DCC)
R-Value Work: 0.135 (Depositor), 0.150 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.8	α = 90
b = 102	β = 90
c = 116.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-05-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-05-24
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.