2FVL | pdb_00002fvl

Crystal structure of human 3-alpha hydroxysteroid/dihydrodiol dehydrogenase (AKR1C4) complexed with NADP+

PDB DOI: https://doi.org/10.2210/pdb2FVL/pdb

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

Deposited: 2006-01-31 Released: 2006-02-21
Deposition Author(s): Ugochukwu, E., Smee, C., Guo, K., Lukacik, P., Kavanagh, K., Debreczeni, J.E., von Delft, F., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.205 (Depositor), 0.167 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (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 3-alpha hydroxysteroid/dihydrodiol dehydrogenase (AKR1C4) complexed with NADP+

Ugochukwu, E., Smee, C., Guo, K., Lukacik, P., Kavanagh, K., Debreczeni, J.E., von Delft, F., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 114.1 kDa
Atom Count: 8,794
Modeled Residue Count: 969
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1, member C4	A, B, C	324	Homo sapiens	Mutation(s): 0 Gene Names: AKR1C4 EC: 1.1.1.225 (PDB Primary Data), 1.1.1.50 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.209 (UniProt), 1.1.1.51 (UniProt), 1.1.1.62 (UniProt), 1.1.1.357 (UniProt), 1.1.1 (UniProt), 1.1.1.210 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P17516 (Homo sapiens) Explore P17516 Go to UniProtKB: P17516
PHAROS: P17516 GTEx: ENSG00000198610
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17516
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 D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.205 (Depositor), 0.167 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.008	α = 90
b = 166.008	β = 90
c = 194.942	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-02-21

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-02-21
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description