2O23

The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A

PDB DOI: https://doi.org/10.2210/pdb2O23/pdb

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

Deposited: 2006-11-29 Released: 2006-12-12
Deposition Author(s): Kavanagh, K.L., Shafqat, N., Scholer, K., Debreczeni, J., Zschocke, J., von Delft, F., Weigelt, J., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.154 (Depositor), 0.160 (DCC)
R-Value Work:
0.123 (Depositor), 0.130 (DCC)
R-Value Observed:
0.123 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A

KAVANAGH, K.L., SHAFQAT, N., SCHOLER, K., DEBRECZENI, J., ZSCHOCKE, J., von Delft, F., WEIGELT, J., ARROWSMITH, C., SUNDSTROM, M., EDWARDS, A., OPPERMANN, U.

To be published.

Macromolecule Content

Total Structure Weight: 55.99 kDa
Atom Count: 4,458
Modelled Residue Count: 503
Deposited Residue Count: 530
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HADH2 protein	A, B	265	Homo sapiens	Mutation(s): 0 Gene Names: HADH2 EC: 1.1.1.178 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.62 (UniProt), 1.1.1.239 (UniProt), 1.1.1.159 (UniProt), 1.1.1.35 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99714 (Homo sapiens) Explore Q99714 Go to UniProtKB: Q99714
PHAROS: Q99714 GTEx: ENSG00000072506
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99714
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.154 (Depositor), 0.160 (DCC)
R-Value Work: 0.123 (Depositor), 0.130 (DCC)
R-Value Observed: 0.123 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.037	α = 90
b = 117.037	β = 90
c = 69.087	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-12-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-31
Changes: Database references, Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description