3KVO

Crystal structure of the catalytic domain of human Hydroxysteroid dehydrogenase like 2 (HSDL2)

PDB DOI: https://doi.org/10.2210/pdb3KVO/pdb

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

Deposited: 2009-11-30 Released: 2010-03-09
Deposition Author(s): Ugochukwu, E., Bhatia, C., Huang, J., Pilka, E., Muniz, J.R.C., Pike, A.C.W., Krojer, T., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Verdin, E.M., Oppermann, U., Kavanagh, K.L., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.247
R-Value Work: 0.199
R-Value Observed: 0.202

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 the catalytic domain of human Hydroxysteroid dehydrogenase like 2 (HSDL2)

Ugochukwu, E., Bhatia, C., Huang, J., Pilka, E., Muniz, J.R.C., Pike, A.C.W., Krojer, T., von Delft, F., Verdin, E.M., Oppermann, U., Kavanagh, K.L.

To be published.

Macromolecule Content

Total Structure Weight: 77.07 kDa
Atom Count: 4,366
Modelled Residue Count: 549
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxysteroid dehydrogenase-like protein 2	A, B	346	Homo sapiens	Mutation(s): 0 Gene Names: HSDL2 EC: 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6YN16 (Homo sapiens) Explore Q6YN16 Go to UniProtKB: Q6YN16
PHAROS: Q6YN16 GTEx: ENSG00000119471
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6YN16
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 C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.247
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.149	α = 90
b = 78.332	β = 90
c = 121.765	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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3KVO

Crystal structure of the catalytic domain of human Hydroxysteroid dehydrogenase like 2 (HSDL2)

Crystal structure of the catalytic domain of human Hydroxysteroid dehydrogenase like 2 (HSDL2)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)