5BQP | pdb_00005bqp

Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus with xanthosine and phosphate bound in the nucleotide binding site and with sulfate bound in the pyrophosphate binding site

PDB DOI: https://doi.org/10.2210/pdb5BQP/pdb

Classification: TRANSFERASE
Organism(s): Saccharolobus solfataricus P2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-05-29 Released: 2015-07-01
Deposition Author(s): Christoffersen, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.162 (Depositor), 0.164 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5BQP

Ligand Structure Quality Assessment

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

Literature

Sulfolobus solfataricus P2

Christoffersen, S., Hansen, M.R., Jensen, K.S., Larsen, S., Jensen, K.F.

To be published.

Macromolecule Content

Total Structure Weight: 85.54 kDa
Atom Count: 6,738
Modeled Residue Count: 682
Deposited Residue Count: 716
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine phosphoribosyltransferase (GpT-2)	A, B, C, D	179	Saccharolobus solfataricus P2	Mutation(s): 0 Gene Names: gpT-2, SSO2424 EC: 2.4.2
UniProt
Find proteins for Q97W22 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W22 Go to UniProtKB: Q97W22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97W22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4UO Query on 4UO Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], N [auth C], S [auth D]	2,3-dihydroxanthosine C₁₀ H₁₂ N₄ O₆ UBORTCNDUKBEOP-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain I [auth A] MOL2 format, chain W [auth D] MOL2 format, chain I [auth A] mmCIF format, chain W [auth D] mmCIF format, chain I [auth A]	I [auth A], W [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain W [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] L [auth B] P [auth C] U [auth D] G [auth A], H [auth A], L [auth B], P [auth C], U [auth D], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], O [auth C], T [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B]	M [auth B], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain M [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.162 (Depositor), 0.164 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.218	α = 90
b = 132.218	β = 90
c = 103.102	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-07-01

Deposition Author(s):

Christoffersen, S.

Revision History (Full details and data files)

Version 1.0: 2015-07-01
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.