3AH5 | pdb_00003ah5

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 (Depositor), 0.245 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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
Modeled Residue Count: 1,250
Deposited Residue Count: 1,296
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 X [auth E] SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain AA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain AA [auth F]	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 W [auth E] SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain BA [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth F]	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 Z [auth E] SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain CA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth F]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246 (Depositor), 0.245 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 221.92	α = 90
b = 49.43	β = 98.84
c = 143.02	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
PHASES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-04-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary