8YI9 | pdb_00008yi9

human PRPS2 isoform2

PDB DOI: https://doi.org/10.2210/pdb8YI9/pdb
EM Map EMD-39312: EMDB EMDataResource

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

Deposited: 2024-02-29 Released: 2025-03-05
Deposition Author(s): Liu, J.L., Lu, G.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8YI9

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

Literature

Structure of human PRPS2 long isoform at 3.4 Angstroms resolution.

Liu, J.L., Lu, G.M.

To be published.

Macromolecule Content

Total Structure Weight: 214.82 kDa
Atom Count: 13,956
Modeled Residue Count: 1,800
Deposited Residue Count: 1,926
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Ribose-phosphate pyrophosphokinase 2	A, B, C, D, E A, B, C, D, E, F	321	Homo sapiens	Mutation(s): 0 Gene Names: PRPS2 EC: 2.7.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11908 (Homo sapiens) Explore P11908 Go to UniProtKB: P11908
PHAROS: P11908 GTEx: ENSG00000101911
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11908
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain S [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain AA [auth F] MOL2 format, chain W [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain W [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth F]	AA [auth F] J [auth A] N [auth B] R [auth C] S [auth D] AA [auth F], J [auth A], N [auth B], R [auth C], S [auth D], W [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain W [auth E]
RP5 (Subject of Investigation/LOI) Query on RP5 Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain BA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth F]	BA [auth F] G [auth A] K [auth B] O [auth C] T [auth D] BA [auth F], G [auth A], K [auth B], O [auth C], T [auth D], X [auth E]	5-O-phosphono-beta-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-TXICZTDVSA-N		Interactions Focus chain BA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain X [auth E]
MG (Subject of Investigation/LOI) Query on MG 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 Q [auth C] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain DA [auth F] 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 Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth F] 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 Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F]	CA [auth F] DA [auth F] H [auth A] I [auth A] L [auth B] CA [auth F], DA [auth F], H [auth A], I [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], U [auth D], V [auth D], Y [auth E], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [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 DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [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: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	No. 31771490

Revision History (Full details and data files)

Version 1.0: 2025-03-05
Type: Initial release
Version 1.1: 2025-07-16
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.