2W98

CRYSTAL STRUCTURE OF HUMAN ZINC-BINDING ALCOHOL DEHYDROGENASE 1 (ZADH1) IN TERNARY COMPLEX WITH NADP AND PHENYLBUTAZONE

PDB DOI: https://doi.org/10.2210/pdb2W98/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-01-22 Released: 2009-04-07
Deposition Author(s): Shafqat, N., Yue, W.W., Muniz, J., Picaud, S., Niesen, F., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.188 (Depositor), 0.220 (DCC)
R-Value Work:
0.158 (Depositor), 0.190 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Human Zinc-Binding Alcohol Dehydrogenase 1

Shafqat, N., Yue, W.W., Niesen, F., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 82.98 kDa
Atom Count: 6,268
Modelled Residue Count: 703
Deposited Residue Count: 714
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROSTAGLANDIN REDUCTASE 2	A, B	357	Homo sapiens	Mutation(s): 0 EC: 1.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8N7 (Homo sapiens) Explore Q8N8N7 Go to UniProtKB: Q8N8N7
PHAROS: Q8N8N7 GTEx: ENSG00000140043
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N8N7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
P1Z Query on P1Z Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A]	D [auth A] E [auth A] F [auth A] K [auth B] L [auth B] D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	4-BUTYL-1,2-DIPHENYL-PYRAZOLIDINE-3,5-DIONE C₁₉ H₂₀ N₂ O₂ VYMDGNCVAMGZFE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
LMR Query on LMR Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	(2S)-2-hydroxybutanedioic acid C₄ H₆ O₅ BJEPYKJPYRNKOW-REOHCLBHSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	G [auth A], H [auth A], I [auth A], O [auth B], P [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.188 (Depositor), 0.220 (DCC)
R-Value Work: 0.158 (Depositor), 0.190 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.014	α = 90
b = 82.793	β = 99.77
c = 69.097	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2013-12-04
Changes: Non-polymer description, Source and taxonomy
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description