6G7X | pdb_00006g7x

Crystal structure of H. pylori purine nucleoside phosphorylase soaked in PO4

PDB DOI: https://doi.org/10.2210/pdb6G7X/pdb

Classification: TRANSFERASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2018-04-06 Released: 2018-08-08
Deposition Author(s): Stefanic, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.193 (Depositor), 0.193 (DCC)
R-Value Work:
0.159 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

The Role of Phosphate Binding in Purine Nucleoside Phosphorylase of Helicobacter pylori

Bosnjakovic, M., Lescic Asler, I., Stefanic, Z.

(2018) Croat Chem Acta 91

DOI: https://doi.org/10.5562/cca3335

Macromolecule Content

Total Structure Weight: 157.07 kDa
Atom Count: 12,053
Modeled Residue Count: 1,398
Deposited Residue Count: 1,398
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase DeoD-type	A, B, C, D, E A, B, C, D, E, F	233	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: deoD, HP_1178 EC: 2.4.2.1
UniProt
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56463 Go to UniProtKB: P56463
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56463
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	DA [auth E] IA [auth F] J [auth A] P [auth B] U [auth C] DA [auth E], IA [auth F], J [auth A], P [auth B], U [auth C], Y [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth E] Focus chain IA [auth F] Focus chain J [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain IA [auth F] Focus chain J [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Y [auth D]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain G [auth A] SDF format, chain GA [auth F] SDF format, chain H [auth A] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth E] BA [auth E] CA [auth E] EA [auth F] FA [auth F] AA [auth E], BA [auth E], CA [auth E], EA [auth F], FA [auth F], G [auth A], GA [auth F], H [auth A], HA [auth F], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D], X [auth D], Z [auth E]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain G [auth A] Focus chain GA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain G [auth A] Focus chain GA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]