4P5A | pdb_00004p5a

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

PDB DOI: https://doi.org/10.2210/pdb4P5A/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: 1.76 Å
R-Value Free:
0.193 (Depositor), 0.160 (DCC)
R-Value Work:
0.154 (Depositor), 0.160 (DCC)
R-Value Observed:
0.156 (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 from Streptomyces cacaoi with 5-Br UMP

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

To be published.

Macromolecule Content

Total Structure Weight: 113.26 kDa
Atom Count: 8,303
Modeled Residue Count: 901
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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D]
5BU Query on 5BU Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], J [auth C], K [auth D]	5-BROMO-URIDINE-5'-MONOPHOSPHATE C₉ H₁₂ Br N₂ O₉ P IDPVUMJNEZFMNU-UAKXSSHOSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth D]