3K1Z | pdb_00003k1z

Crystal Structure of Human Haloacid Dehalogenase-like Hydrolase Domain containing 3 (HDHD3)

• PDB DOI: https://doi.org/10.2210/pdb3K1Z/pdb

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


• Deposited: 2009-09-29 Released: 2009-11-03 
• Deposition Author(s): Ugochukwu, E., Guo, K., Yue, W.W., Pilka, E., Picaud, S., Muniz, J., Pike, A.C.W., Krojer, T., Gomes, M., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Kavanagh, K., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.207 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal Structure of Human Haloacid Dehalogenase-like Hydrolase Domain containing 3 (HDHD3)

Ugochukwu, E., Guo, K., Yue, W.W., Pilka, E., Kavanagh, K., Oppermann, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.02 kDa 
• Atom Count: 2,257 
• Modelled Residue Count: 241 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase-like hydrolase domain-containing protein 3	A	263	Homo sapiens	Mutation(s): 0  Gene Names: HDHD3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSH5 (Homo sapiens) Explore Q9BSH5  Go to UniProtKB:  Q9BSH5
PHAROS:  Q9BSH5 GTEx:  ENSG00000119431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.207 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.625	α = 90
b = 62.455	β = 90
c = 79.665	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Ugochukwu, E., Guo, K., Yue, W.W., Pilka, E., Picaud, S., Muniz, J., Pike, A.C.W., Krojer, T., Gomes, M., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Kavanagh, K., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2024-10-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary