7WUO

Unravelling structure of riboflavin synthase for designing of potential anti-bacterial drug

PDB DOI: https://doi.org/10.2210/pdb7WUO/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Leptospira kmetyi serovar Malaysia str. Bejo-Iso9
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-09 Released: 2022-06-15
Deposition Author(s): Aris, S.N.A.M., Leow, A.T.C., Motomura, T., Jonet, M.A.
Funding Organization(s): Ministry of Science, Technology and Innovation (MOSTI, Malaysia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free: 0.264
R-Value Work: 0.218
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Unraveling the crystal structure of Leptospira kmetyi riboflavin synthase and computational analyses for potential development of new antibacterials

Aris, S.N.A.M., Rahman, R.N.Z.R.A., Ali, M.S.M., Jonet, M.A., Motomura, T., Noor, N.D.M., Shariff, F.M., Hsu, K.C., Chor, L.T.

(2022) J Mol Struct : 133420

DOI: https://doi.org/10.1016/j.molstruc.2022.133420

Macromolecule Content

Total Structure Weight: 69.89 kDa
Atom Count: 4,645
Modelled Residue Count: 603
Deposited Residue Count: 627
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin synthase	A, B, C	209	Leptospira kmetyi serovar Malaysia str. Bejo-Iso9	Mutation(s): 0 Gene Names: EHQ67_13285 EC: 2.5.1.9
UniProt
Find proteins for A0A7I0ICZ8 (Leptospira kmetyi) Explore A0A7I0ICZ8 Go to UniProtKB: A0A7I0ICZ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7I0ICZ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth C] MOL2 format, chain D [auth B] MOL2 format, chain E [auth C]	D [auth B], E [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth C] Interactions & Density Focus chain D [auth B] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free: 0.264
R-Value Work: 0.218
R-Value Observed: 0.220
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.559	α = 90
b = 130.632	β = 90
c = 202.5	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science, Technology and Innovation (MOSTI, Malaysia)	Malaysia	02-01-04-SF1321

Revision History (Full details and data files)

Version 1.0: 2022-06-15
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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 R01GM133198.