6C5Z | pdb_00006c5z

Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-glucose and NADH bound

PDB DOI: https://doi.org/10.2210/pdb6C5Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-01-17 Released: 2019-01-23
Deposition Author(s): Gross, P.G., Sidlo, A.M., Walsh, R.M., Peeples, W.B., Wood, Z.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.203 (Depositor), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The A225L Substitution of hUGDH alters structure and function

Gross, P.G., Wood, Z.A.

To be published.

Macromolecule Content

Total Structure Weight: 337.54 kDa
Atom Count: 21,261
Modeled Residue Count: 2,612
Deposited Residue Count: 2,964
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 6-dehydrogenase	A, B, C, D, E A, B, C, D, E, F	494	Homo sapiens	Mutation(s): 1 Gene Names: UGDH EC: 1.1.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for O60701 (Homo sapiens) Explore O60701 Go to UniProtKB: O60701
PHAROS: O60701 GTEx: ENSG00000109814
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60701
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain P [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F]	G [auth A], J [auth C], L [auth D], N [auth E], P [auth F]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain P [auth F]
UPG Query on UPG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F]	H [auth A] I [auth B] K [auth C] M [auth D] O [auth E] H [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.203 (Depositor), 0.205 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.77	α = 90
b = 199.8	β = 90
c = 200.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM114298

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary