SMTL ID : 8qhq.3 (2 other biounits)

Crystal structure of human DNPH1 bound to hmdUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

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

5HU.1: 19 residues within 4Å: Chain A: F.10, C.11, G.12, S.13, I.14, R.15, G.16, H.41, V.42, I.61, D.65, S.83, L.84, G.85, V.86, Q.89 Chain B: S.113, A.114, M.115 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.14, A:V.42, B:A.114 Hydrogen bonds: A:G.12, A:I.14, A:R.15, A:G.16, A:H.41, A:S.83, A:L.84, A:G.85, A:V.86, A:Q.89, B:A.114 Water bridges: A:S.83 5HU.3: 19 residues within 4Å: Chain A: S.113, A.114, M.115 Chain B: F.10, C.11, G.12, S.13, I.14, R.15, G.16, H.41, V.42, I.61, D.65, S.83, L.84, G.85, V.86, Q.89 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.42, A:A.114 Hydrogen bonds: B:G.12, B:I.14, B:R.15, B:G.16, B:H.41, B:S.83, B:L.84, B:G.85, B:V.86, B:Q.89, A:A.114 Water bridges: B:R.15, B:S.83

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: S.29, R.30, R.33, E.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.29, A:R.30 Water bridges: A:R.30, A:E.136 EDO.4: 4 residues within 4Å: Chain B: S.29, R.30, R.33, E.136 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.29, B:R.30 Water bridges: B:R.30, B:R.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rzechorzek, N.J. et al., Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1. Nat Commun (2023)

Release Date

2023-11-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

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

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