8WXK | pdb_00008wxk

Crystal Structure of UDP-Glucose 4-Epimerase (all4713) with UDP-glucose and NAD from Nostoc sp. PCC 7120

PDB DOI: https://doi.org/10.2210/pdb8WXK/pdb

Classification: ISOMERASE
Organism(s): Nostoc sp. PCC 7120 = FACHB-418
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-30 Released: 2024-10-30
Deposition Author(s): Su, J.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.229 (Depositor), 0.227 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (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

Crystal Structure of UDP-Glucose 4-Epimerase (all4713) with UDP-glucose and NAD from Nostoc sp. PCC 7120

Su, J.Y.

To be published.

Macromolecule Content

Total Structure Weight: 150.58 kDa
Atom Count: 10,829
Modelled Residue Count: 1,318
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase	A, B, C, D	332	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Gene Names: all4713 EC: 5.1.3.2
UniProt
Find proteins for Q8YN57 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YN57 Go to UniProtKB: Q8YN57
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YN57
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	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]
UPG Query on UPG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-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]