› 4l1j

X-ray diffraction
1.82Å resolution

Three dimensional structure of mutant D143A of human HD domain-containing protein 2, Northeast Structural Genomics Consortium (NESG) Target HR6723

Released:
DOI: 10.2210/pdb4l1j/pdb
PDB entry 4l1j coloured by chain, front view.
PDB entry 4l1j coloured by chain, side view.
PDB entry 4l1j coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Kuzin A, Su M, Yakunin A, Beloglazova O, Seetharaman J, Maglaqui M, Xiao R, Lee D, Brown G, Flick R, Everett JK, Acton TB, Montelione GT, Hunt JF, Tong L, Northeast Structural Genomics Consortium (NESG)

Function and Biology Details

Reaction catalysed: 
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182266 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
5'-deoxynucleotidase HDDC2 Chain: A
Molecule details ›
Chain: A
Length: 204 amino acids
Theoretical weight: 23.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7Z4H3 (Residues: 1-204; Coverage: 100%)
Gene names: C6orf74, CGI-130, HDDC2, NS5ATP2
Sequence domains: HD domain
Structure domains: Hypothetical protein af1432
5'-deoxynucleotidase HDDC2 Chain: B
Molecule details ›
Chain: B
Length: 204 amino acids
Theoretical weight: 23.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7Z4H3 (Residues: 1-204; Coverage: 100%)
Gene names: C6orf74, CGI-130, HDDC2, NS5ATP2
Sequence domains: HD domain
Structure domains: Hypothetical protein af1432

Ligands and Environments

2 bound ligands:
Ligand PEG 6 x PEG
Ligand PE4 1 x PE4
2 modified residues:
Ligand MSE 16 x MSE
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: P212121
Unit cell:
a: 64.991Å b: 69.929Å c: 105.778Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.176 0.201
Expression system: Escherichia coli BL21(DE3)

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