8Q2I | pdb_00008q2i

Crystal structure of Ser33 in complex 2HG (2-hydroxyglutarate) and Serine

PDB DOI: https://doi.org/10.2210/pdb8Q2I/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-08-02 Released: 2025-02-12
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: 2.51 Å
R-Value Free:
0.253 (Depositor), 0.252 (DCC)
R-Value Work:
0.236 (Depositor), 0.236 (DCC)

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 2HG (2-hydroxyglutarate) and 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: 416.68 kDa
Atom Count: 27,369
Modelled Residue Count: 3,497
Deposited Residue Count: 3,752
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase 2	A, B, C, D, E A, B, C, D, E, F, G, H	469	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% 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 AA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain U [auth F] SDF format, chain X [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] MOL2 format, chain X [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain U [auth F] mmCIF format, chain X [auth G]	AA [auth H] I [auth A] L [auth B] N [auth C] P [auth D] AA [auth H], I [auth A], L [auth B], N [auth C], P [auth D], R [auth E], U [auth F], X [auth G]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain U [auth F] Focus chain X [auth G] Interactions & Density Focus chain AA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain U [auth F] Focus chain X [auth G]
2HG (Subject of Investigation/LOI) Query on 2HG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] MOL2 format, chain K [auth A] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain K [auth A] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G]	K [auth A], T [auth E], W [auth F], Z [auth G]	(2R)-2-hydroxypentanedioic acid C₅ H₈ O₅ HWXBTNAVRSUOJR-GSVOUGTGSA-N		Interactions Focus chain K [auth A] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain K [auth A] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G]
SER (Subject of Investigation/LOI) Query on SER Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain J [auth A] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain Y [auth G] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain V [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain Y [auth G] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain V [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain Y [auth G] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain V [auth F]	BA [auth H] J [auth A] M [auth B] O [auth C] Q [auth D] BA [auth H], J [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], V [auth F], Y [auth G]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain BA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F] Focus chain Y [auth G]