SMTL ID : 8qhr.1

Crystal structure of the human DNPH1 glycosyl-enzyme intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x 3DR: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE(Covalent)

3DR.1: 17 residues within 4Å: Chain A: Y.9, C.11, G.12, S.13, I.14, R.15, G.16, Q.40, H.41, D.65, S.83, L.84, G.85, V.86, E.89 Chain B: S.113, M.115 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.12, A:I.14, A:R.15, A:G.16, A:H.41, A:S.83, A:S.83, A:L.84, A:G.85, A:V.86, A:E.89, B:S.113 Water bridges: A:Q.40 3DR.4: 18 residues within 4Å: Chain A: S.113, A.114, M.115 Chain B: Y.9, C.11, G.12, S.13, I.14, R.15, G.16, Q.40, H.41, D.65, S.83, L.84, G.85, V.86, E.89 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.12, B:I.14, B:R.15, B:G.16, B:H.41, B:S.83, B:S.83, B:L.84, B:G.85, B:V.86, B:E.89, A:S.113 Water bridges: A:A.114, A:M.115, A:M.115

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

EDO.2: 6 residues within 4Å: Chain A: A.72, D.73, F.96, N.97, K.98, R.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.98 Water bridges: A:D.73 EDO.3: 3 residues within 4Å: Chain A: W.128, L.138, R.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.141

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.5: 3 residues within 4Å: Chain B: L.60, Q.64, E.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.64, B:E.67 Water bridges: B:L.60

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