SMTL ID : 8rqd.1

Crystal structure of human DNPH1 mutant-Y24F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: S.81, L.82 Chain B: P.80 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: A.118, G.120, F.123, Q.124, V.125 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: R.16 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: E.129 Ligand excluded by PLIP

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 1 residues within 4Å: Chain A: M.2 No protein-ligand interaction detected (PLIP) PEG.5: 4 residues within 4Å: Chain A: V.72, R.97, Y.140, F.141 No protein-ligand interaction detected (PLIP) PEG.6: 6 residues within 4Å: Chain A: G.116, A.117, A.118, D.119 Chain B: R.57, H.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.57 Water bridges: B:H.60 PEG.8: 5 residues within 4Å: Chain B: E.38, L.45, L.58, I.59, Q.62 No protein-ligand interaction detected (PLIP) PEG.9: 9 residues within 4Å: Chain A: P.80, V.109, L.110, S.111 Chain B: S.11, I.12, P.80, S.81, L.82 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.12, B:L.82, A:S.111 PEG.10: 3 residues within 4Å: Chain B: E.61, Q.62, E.65 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.65

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 6 residues within 4Å: Chain B: L.45, E.51, A.52, A.53, G.54, G.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.52, B:G.55

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
A

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