3HLT | pdb_00003hlt

The crystal structure of human haloacid dehalogenase-like hydrolase domain containing 2 (HDHD2)

• PDB DOI: https://doi.org/10.2210/pdb3HLT/pdb

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


• Deposited: 2009-05-28 Released: 2009-07-07 
• Deposition Author(s): Ugochukwu, E., Shafqat, N., Yue, W.W., Cocking, R., Bray, J.E., Muniz, J.R.C., Krojer, T., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of human haloacid dehalogenase-like hydrolase domain containing 2 (HDHD2)

Ugochukwu, E., Shafqat, N., Yue, W.W., Cocking, R., Bray, J.E., Muniz, J.R.C., Krojer, T., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., 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.

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)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.19 kDa 
• Atom Count: 3,742 
• Modeled Residue Count: 499 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HDHD2	A, B [auth C]	266	Homo sapiens	Mutation(s): 0  Gene Names: HDHD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0R4 (Homo sapiens) Explore Q9H0R4  Go to UniProtKB:  Q9H0R4
PHAROS:  Q9H0R4 GTEx:  ENSG00000167220

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], G [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.94	α = 90
b = 77.68	β = 90
c = 103.99	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: 2009-07-07 
Deposition Author(s): Ugochukwu, E., Shafqat, N., Yue, W.W., Cocking, R., Bray, J.E., Muniz, J.R.C., Krojer, T., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, 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