3AH5

Crystal Structure of flavin dependent thymidylate synthase ThyX from helicobacter pylori complexed with FAD and dUMP

PDB DOI: https://doi.org/10.2210/pdb3AH5/pdb

Classification: TRANSFERASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-04-14 Released: 2011-04-20
Deposition Author(s): Zhang, X., Zhang, J., Hu, Y., Zou, Q., Wang, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246
R-Value Work: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure and functional analysis of a flavin dependent thymidylate synthase from helicobacter pylori

Zhang, X., Zhang, J., Hu, Y., Zou, Q., Wang, D.

To be published.

Macromolecule Content

Total Structure Weight: 158.69 kDa
Atom Count: 11,206
Modelled Residue Count: 1,250
Deposited Residue Count: 1,296
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, E A, B, C, D, E, F	216	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: HP_1533, thyX EC: 2.1.1.148
UniProt
Find proteins for O26061 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O26061 Go to UniProtKB: O26061
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O26061
Sequence Annotations Expand
Reference Sequence

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 AA [auth F] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] MOL2 format, chain X [auth E]	AA [auth F] H [auth A] M [auth B] N [auth C] S [auth D] AA [auth F], H [auth A], M [auth B], N [auth C], S [auth D], X [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain AA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain X [auth E]
UMP Query on UMP Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E]	BA [auth F] G [auth A] L [auth B] O [auth C] T [auth D] BA [auth F], G [auth A], L [auth B], O [auth C], T [auth D], W [auth E]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain BA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain BA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain W [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E]	CA [auth F] I [auth A] J [auth A] K [auth A] P [auth C] CA [auth F], I [auth A], J [auth A], K [auth A], P [auth C], Q [auth C], R [auth C], U [auth D], V [auth D], Y [auth E], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Focus chain Z [auth E]