8YPZ | pdb_00008ypz

Crystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb8YPZ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-18 Released: 2025-03-19
Deposition Author(s): Zhang, L., Zhang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 ?
R-Value Free:
0.310 (Depositor), 0.317 (DCC)
R-Value Work:
0.260 (Depositor), 0.283 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP

Zhang, L., Zhang, L.

To be published.

Macromolecule Content

Total Structure Weight: 216.42 kDa
Atom Count: 14,526
Modelled Residue Count: 1,835
Deposited Residue Count: 1,908
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-phosphate pyrophosphokinase 1	A, B, C, D, E A, B, C, D, E, F	318	Homo sapiens	Mutation(s): 0 Gene Names: PRPS1 EC: 2.7.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60891 (Homo sapiens) Explore P60891 Go to UniProtKB: P60891
PHAROS: P60891 GTEx: ENSG00000147224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60891
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APC Query on APC Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	G [auth A] K [auth A] M [auth B] P [auth C] U [auth D] G [auth A], K [auth A], M [auth B], P [auth C], U [auth D], X [auth E]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain G [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain U [auth D] Focus chain X [auth E]
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth E]	AA [auth F] I [auth A] J [auth A] R [auth C] S [auth C] AA [auth F], I [auth A], J [auth A], R [auth C], S [auth C], Z [auth E]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain AA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth E]
HSX Query on HSX Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain BA [auth F] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C]	BA [auth F], H [auth A], N [auth B], Q [auth C], Y [auth E]	5-O-phosphono-alpha-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-AIHAYLRMSA-N		Interactions Focus chain BA [auth F] Focus chain H [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain H [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain Y [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain CA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	CA [auth F] L [auth A] O [auth B] T [auth C] V [auth D] CA [auth F], L [auth A], O [auth B], T [auth C], V [auth D], W [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth F] Focus chain L [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain CA [auth F] Focus chain L [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D]