8PIO | pdb_00008pio

Crystal structure of Ser33 in complex with PHP (3-phosphohydroxypyruvate)

PDB DOI: https://doi.org/10.2210/pdb8PIO/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-22 Released: 2025-01-15
Deposition Author(s): Perrone, S., Cifuente, J.O., Marina, A., Mastrella, L., Trastoy, B., Linster, C.L., Guerin, M.E.
Funding Organization(s): Ministry of Economy and Competitiveness (MINECO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.262 (Depositor), 0.262 (DCC)
R-Value Work:
0.222 (Depositor), 0.223 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Ser33 in complex with PHP (3-phosphohydroxypyruvate)

Perrone, S., Cifuente, J.O., Marina, A., Mastrella, L., Trastoy, B., Linster, C.L., Guerin, M.E.

To be published.

Macromolecule Content

Total Structure Weight: 208.73 kDa
Atom Count: 13,225
Modeled Residue Count: 1,748
Deposited Residue Count: 1,876
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphoglycerate dehydrogenase	A [auth F], B [auth A], C [auth B], D [auth C]	469	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SER33 EC: 1.1.1.399 (UniProt), 1.1.1.95 (UniProt)
UniProt
Find proteins for P40510 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40510 Go to UniProtKB: P40510
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40510
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain E [auth F] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain E [auth F] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain E [auth F]	E [auth F], H [auth A], K [auth B], N [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth F] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain E [auth F] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C]
HPV (Subject of Investigation/LOI) Query on HPV Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain F MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain F mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain F	F, J [auth A], M [auth B], P [auth C]	2-oxo-3-(phosphonooxy)propanoic acid C₃ H₅ O₇ P LFLUCDOSQPJJBE-UHFFFAOYSA-N		Interactions Focus chain F Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Interactions & Density Focus chain F Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], I [auth A], L [auth B], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C]