8PIS | pdb_00008pis

Crystal structure of Ser33 in complex with L-Serine

PDB DOI: https://doi.org/10.2210/pdb8PIS/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: 2.69 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.216 (Depositor), 0.217 (DCC)
R-Value Observed:
0.218 (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 L-Serine

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: 425.22 kDa
Atom Count: 26,154
Modeled Residue Count: 3,493
Deposited Residue Count: 3,864
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphoglycerate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	473	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% 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
phosphoglycerate dehydrogenase	I J K L [auth M] M [auth N] I, J, K, L [auth M], M [auth N], N [auth O], O [auth Q], P [auth L]	10	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 BA [auth F] SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth E] SDF format, chain W [auth D] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D]	BA [auth F] CA [auth G] EA [auth H] Q [auth A] S [auth B] BA [auth F], CA [auth G], EA [auth H], Q [auth A], S [auth B], U [auth C], W [auth D], Y [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E]
SER Query on SER Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain R [auth A] SDF format, chain FA [auth H] SDF format, chain DA [auth G] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain R [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain R [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth E]	AA [auth E] DA [auth G] FA [auth H] R [auth A] T [auth B] AA [auth E], DA [auth G], FA [auth H], R [auth A], T [auth B], V [auth C], X [auth D], Z [auth E]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]