SMTL ID : 8rpt.1

Crystal structure of human DNPH1 mutant- D80A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

8 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: 3 residues within 4Å: Chain A: G.14, R.16, E.17 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: P.80 Chain B: S.81, L.82 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: G.54, G.55, D.56, R.57 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: R.103, Q.105, E.129, E.130 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: W.66 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: A.118, G.120, Q.124, V.125 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: A.93 Chain B: R.90, A.93, F.94 Ligand excluded by PLIP

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

PEG.3: 5 residues within 4Å: Chain A: A.43, E.44, L.45, G.46, A.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.43, A:A.47 PEG.12: 4 residues within 4Å: Chain B: V.125, W.126, D.127, R.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.125, B:D.127, B:R.139

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

EDO.4: 3 residues within 4Å: Chain A: A.42, A.43, G.46 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.42, A:G.49 EDO.5: 6 residues within 4Å: Chain A: G.10, S.11, D.18, Y.22, E.76, R.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.11, A:D.18, A:R.103 EDO.13: 5 residues within 4Å: Chain A: S.111, M.113 Chain B: G.10, E.38, G.83 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.10, A:S.111, A:M.113 Water bridges: B:G.10, B:S.81, B:G.83, A:A.112 EDO.14: 2 residues within 4Å: Chain B: P.104, Q.105 No protein-ligand interaction detected (PLIP)

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
B

B
A

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