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
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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
Modelled Residue Count: 1,748
Deposited Residue Count: 1,876
Unique protein chains: 1

Macromolecules

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(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 E [auth F] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain E [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] mmCIF format, chain E [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C]	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 F SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] MOL2 format, chain F MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] mmCIF format, chain F mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C]	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 G [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C]	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]