4P5B

Crystal structure of a UMP/dUMP methylase PolB from Streptomyces cacaoi bound with 5-Br dUMP

PDB DOI: https://doi.org/10.2210/pdb4P5B/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces asoensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-03-15 Released: 2015-12-09
Deposition Author(s): Li, Y., Chen, W., Li, J., Xia, Z., Deng, Z., Zhou, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.216 (Depositor), 0.210 (DCC)
R-Value Work:
0.164 (Depositor), 0.160 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a UMP/dUMP methylase PolB form Streptomyces cacaoi bound with 5-Br dUMP

Li, Y., Chen, W., Li, J., Xia, Z., Deng, Z., Zhou, J.

To be published.

Macromolecule Content

Total Structure Weight: 113.29 kDa
Atom Count: 8,125
Modelled Residue Count: 933
Deposited Residue Count: 956
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase ThyX	A, B, C, D	239	Streptomyces asoensis	Mutation(s): 0 Gene Names: polB, thyX EC: 2.1.1.148
UniProt
Find proteins for C1IC19 (Streptomyces asoensis) Explore C1IC19 Go to UniProtKB: C1IC19
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1IC19
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D]	E [auth A], I [auth B], J [auth C], M [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D]
BRU Query on BRU Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], K [auth C], L [auth D]	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE C₉ H₁₂ Br N₂ O₈ P LHLHVDBXXZVYJT-RRKCRQDMSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]