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

This is version 1.0 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
Modelled Residue Count: 1,800
Deposited Residue Count: 1,926
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11908
Sequence Annotations Expand
Reference Sequence LOADING

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