3L5K | pdb_00003l5k

The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)

• PDB DOI: https://doi.org/10.2210/pdb3L5K/pdb

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


• Deposited: 2009-12-22 Released: 2010-03-09 
• Deposition Author(s): Ugochukwu, E., Guo, K., Picaud, S., Muniz, J., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Yue, W.W., Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.213 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Models: experimental

Literature

The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)

Ugochukwu, E., Guo, K., Picaud, S., Muniz, J., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Yue, W.W., Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

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: 28.21 kDa 
• Atom Count: 2,063 
• Modeled Residue Count: 233 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase-like hydrolase domain-containing protein 1A	A	250	Homo sapiens	Mutation(s): 0  Gene Names: HDHD1A EC: 3.1.3.96
UniProt & NIH Common Fund Data Resources
Find proteins for Q08623 (Homo sapiens) Explore Q08623  Go to UniProtKB:  Q08623
PHAROS:  Q08623 GTEx:  ENSG00000130021

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.213 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.19	α = 90
b = 85.19	β = 90
c = 103.03	γ = 120

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., Guo, K., Picaud, S., Muniz, J., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Yue, W.W., Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: 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