2VNA | pdb_00002vna

Structure of Human Zinc-binding Alcohol Dehydrogenase 1 (ZADH1)

PDB DOI: https://doi.org/10.2210/pdb2VNA/pdb

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

Deposited: 2008-02-01 Released: 2009-02-17
Deposition Author(s): Shafqat, N., Kavanagh, K., Pike, A.C.W., Muniz, J.R.C., Pilka, E., Roos, A.K., Picaud, S., Johansson, C., Smee, C., Fedorov, O., Kochan, G., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., von Delft, F., Opperman, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.226 (Depositor), 0.225 (DCC)
R-Value Work:
0.189 (Depositor), 0.186 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure of Human Zinc-Binding Alcohol Dehydrogenase 1 (Zadh1)

Shafqat, N., Kavanagh, K., Pike, A.C.W., Muniz, J.R.C., Pilka, E., Roos, A.K., Picaud, S., Johansson, C., Smee, C., Fedorov, O., Kochan, G., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., von Delft, F., Opperman, U.

To be published.

Macromolecule Content

Total Structure Weight: 40.08 kDa
Atom Count: 2,785
Modeled Residue Count: 349
Deposited Residue Count: 357
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROSTAGLANDIN REDUCTASE 2	A	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N8N7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.226 (Depositor), 0.225 (DCC)
R-Value Work: 0.189 (Depositor), 0.186 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.335	α = 90
b = 83.505	β = 108.43
c = 72.585	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-02-17
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2019-09-18
Changes: Data collection
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description