3KVO | pdb_00003kvo

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.247 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.247 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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