SMTL ID : 8rps.1 (1 other biounit)

Crystal structure of human DNPH1 mutant- D80N bound to 5hmdUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x 5HU: 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE(Non-covalent)

5HU.1: 17 residues within 4Å: Chain A: C.9, G.10, S.11, I.12, R.13, G.14, E.38, I.59, N.63, S.81, L.82, G.83, V.84, E.87 Chain B: S.111, A.112, M.113 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.12, B:A.112 Hydrogen bonds: A:G.10, A:G.10, A:I.12, A:R.13, A:R.13, A:R.13, A:G.14, A:E.38, A:N.63, A:L.82, A:G.83, A:V.84, B:A.112 Water bridges: A:Y.7, A:R.13, A:S.81 5HU.2: 17 residues within 4Å: Chain A: S.111, A.112, M.113 Chain B: C.9, G.10, S.11, I.12, R.13, G.14, E.38, I.59, N.63, S.81, L.82, G.83, V.84, E.87 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.12, A:A.112 Hydrogen bonds: B:G.10, B:G.10, B:I.12, B:R.13, B:R.13, B:R.13, B:G.14, B:E.38, B:E.38, B:N.63, B:L.82, B:G.83, B:V.84, A:A.112 Water bridges: B:R.13, B:S.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carberry, A.E. et al., Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80. Chembiochem (2024)

Release Date

2024-11-20

Peptides

2'-deoxynucleoside 5'-phosphate N-hydrolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

2'-deoxynucleoside 5'-phosphate N-hydrolase 1

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