2PD6

Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8

PDB DOI: https://doi.org/10.2210/pdb2PD6/pdb

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

Deposited: 2007-03-31 Released: 2007-05-08
Deposition Author(s): Turnbull, A.P., Salah, E., Gileadi, O., Savitsky, P., Guo, K., Bunkoczi, G., Pike, A.C.W., Ugochukwu, E., Umeano, C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.227 (Depositor), 0.240 (DCC)
R-Value Work:
0.184 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

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

Literature

Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8

Turnbull, A.P., Salah, E., Gileadi, O., Savitsky, P., Guo, K., Bunkoczi, G., Pike, A.C.W., Ugochukwu, E., Umeano, C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 112.52 kDa
Atom Count: 7,000
Modelled Residue Count: 953
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estradiol 17-beta-dehydrogenase 8	A, B, C, D	264	Homo sapiens	Mutation(s): 0 Gene Names: HSD17B8, FABGL, HKE6, RING2 EC: 1.1.1.62 (PDB Primary Data), 1.1.1.239 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92506 (Homo sapiens) Explore Q92506 Go to UniProtKB: Q92506
PHAROS: Q92506 GTEx: ENSG00000204228
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92506
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.227 (Depositor), 0.240 (DCC)
R-Value Work: 0.184 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.839	α = 90
b = 62.429	β = 99.22
c = 102.439	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-05-08

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-05-08
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: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description