3COS

Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex with NAD and Zn

PDB DOI: https://doi.org/10.2210/pdb3COS/pdb

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

Deposited: 2008-03-29 Released: 2008-04-15
Deposition Author(s): Kavanagh, K.L., Shafqat, N., Yue, W., von Delft, F., Bishop, S., Roos, A., Murray, J., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (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 class II alcohol dehydrogenase (ADH4) in complex with NAD and Zn.

Kavanagh, K.L., Shafqat, N., Yue, W., von Delft, F., Bishop, S., Roos, A., Murray, J., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 165.33 kDa
Atom Count: 12,141
Modelled Residue Count: 1,518
Deposited Residue Count: 1,524
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase 4	A, B, C, D	381	Homo sapiens	Mutation(s): 0 Gene Names: ADH4 EC: 1.1.1.1 (PDB Primary Data), 1.1.1.105 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P08319 (Homo sapiens) Explore P08319 Go to UniProtKB: P08319
PHAROS: P08319 GTEx: ENSG00000198099
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08319
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth C] SDF format, chain M [auth B] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain T [auth C] MOL2 format, chain M [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain T [auth C] mmCIF format, chain M [auth B] mmCIF format, chain Y [auth D]	G [auth A], M [auth B], T [auth C], Y [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain W [auth D]	E [auth A] F [auth A] K [auth B] L [auth B] R [auth C] E [auth A], F [auth A], K [auth B], L [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth D]	AA [auth D] H [auth A] I [auth A] N [auth B] O [auth B] AA [auth D], H [auth A], I [auth A], N [auth B], O [auth B], U [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain Z [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain P [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B]	BA [auth D], J [auth A], P [auth B], Q [auth B], V [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.299	α = 90
b = 160.919	β = 111.64
c = 88.739	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-04-15

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-04-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description