8PIN | pdb_00008pin

Crystal structure of Ser33

PDB DOI: https://doi.org/10.2210/pdb8PIN/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: 3.19 Å
R-Value Free:
0.284 (Depositor), 0.281 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (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

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

To be published.

Macromolecule Content

Total Structure Weight: 190.74 kDa
Atom Count: 11,800
Modeled Residue Count: 1,708
Deposited Residue Count: 1,720
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase 2	A, B [auth C], C [auth D], D [auth B]	424	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SER33, YIL074C EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (PDB Primary Data)
UniProt
Find proteins for P40510 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40510 Go to UniProtKB: P40510
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40510
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Poli-ALA	E [auth F], F [auth G], G [auth H]	8	Saccharomyces cerevisiae	Mutation(s): 0

Small Molecules

Ligands 2 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 B] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth A]	H [auth A], J [auth C], L [auth D], N [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth B]
PI (Subject of Investigation/LOI) Query on PI Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A]	I [auth A], K [auth C], M [auth D], O [auth B]	HYDROGENPHOSPHATE ION H O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth B]