8RDI | pdb_00008rdi

Crystal structure of UDP-galactose 4-epimerase from Pyrococcus horikoshii containing Y145F mutation and with bound NAD and GDP-L-fucose

PDB DOI: https://doi.org/10.2210/pdb8RDI/pdb

Classification: ISOMERASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-12-08 Released: 2024-12-18
Deposition Author(s): Thunnissen, A.M.W.H., Alvarez Quispe, C., Desmet, T.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.290 (Depositor), 0.275 (DCC)
R-Value Work:
0.220 (Depositor)
R-Value Observed:
0.223 (Depositor)

Starting Model: in silico
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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

Structural, computational and biochemical analysis reveal new insights in the specificity of a promiscuous GDP-Gal4E

Alvarez Quispe, C., Savino, S., Biarnes, X., Planas, A., Thunnissen, A.M.W.H., Beerens, K., Desmet, T.

To be published.

Macromolecule Content

Total Structure Weight: 151.79 kDa
Atom Count: 10,296
Modeled Residue Count: 1,264
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family NAD(P)-dependent oxidoreductase	A, B, C, D	326	Pyrococcus horikoshii	Mutation(s): 1 Gene Names: HA331_04725
UniProt
Find proteins for O73960 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O73960 Go to UniProtKB: O73960
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O73960
Sequence Annotations Expand
Reference Sequence

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 K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
GFB (Subject of Investigation/LOI) Query on GFB Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C]	F [auth A], H [auth B], J [auth C], L [auth D]	GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE C₁₆ H₂₅ N₅ O₁₅ P₂ LQEBEXMHBLQMDB-JGQUBWHWSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]