SMTL ID : 8qhq.1 (2 other biounits)

Crystal structure of human DNPH1 bound to hmdUMP

Coordinates

PDB Format

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: 20 residues within 4Å: Chain A: F.10, C.11, G.12, S.13, I.14, R.15, G.16, H.41, V.42, L.47, I.61, D.65, S.83, L.84, G.85, V.86, Q.89 Chain B: S.113, A.114, M.115 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: 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:S.113, B:A.114 Water bridges: A:F.10, A:R.15, A:T.39, 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 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:S.113, A:A.114 Water bridges: B:R.15, B:S.83

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

EDO.2: 9 residues within 4Å: Chain A: V.94, A.119, D.121, F.125 Chain B: R.59, H.62, E.63, Y.88, R.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.59, B:H.62 Water bridges: B:R.59 EDO.4: 6 residues within 4Å: Chain B: S.123, Q.126, W.128, Y.142, A.145, D.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.126, B:Y.142 EDO.5: 3 residues within 4Å: Chain B: R.26, G.133, E.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.133 EDO.6: 10 residues within 4Å: Chain A: R.59, H.62, E.63, Y.88, R.92 Chain B: V.94, G.118, A.119, D.121, F.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.59, A:H.62

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
A

B
B

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

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