SMTL ID : 1ak0.1

P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: W.55, N.92, Y.93, R.96, E.109 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: N.197, S.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.199 NAG.3: 2 residues within 4Å: Chain A: N.138, Q.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.138

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: D.45, R.48, H.60, H.116, D.120 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.45, A:H.60, A:H.116, A:D.120 ZN.5: 4 residues within 4Å: Chain A: H.126, H.149, D.153 Ligands: THS.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.126, A:H.149, A:D.153, A:D.153 ZN.6: 4 residues within 4Å: Chain A: W.1, H.6, D.120 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:W.1, A:H.6, A:D.120 ZN.7: 2 residues within 4Å: Chain A: H.15, E.181 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.15, A:E.181, A:E.181, H2O.6

1 x ADS: ADENOSINE-5'-(DITHIO)PHOSPHATE(Non-functional Binders)

ADS.8: 1 residues within 4Å: Ligands: THS.9 No protein-ligand interaction detected (PLIP)

3 x THS: THYMIDINE-5'-(DITHIO)PHOSPHATE(Non-functional Binders)(Non-covalent)

THS.9: 2 residues within 4Å: Ligands: ADS.8, THS.10 No protein-ligand interaction detected (PLIP) THS.10: 4 residues within 4Å: Chain A: N.135, K.136 Ligands: THS.9, THS.11 No protein-ligand interaction detected (PLIP) THS.11: 11 residues within 4Å: Chain A: R.48, F.61, D.63, L.125, H.126, V.132, N.135, H.149, D.153 Ligands: ZN.5, THS.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.61, A:V.132 Hydrogen bonds: A:D.63, A:N.135 Water bridges: A:D.63 pi-Stacking: A:F.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romier, C. et al., Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs. Proteins (1998)

Release Date

1997-12-03

Peptides

P1 NUCLEASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

P1 NUCLEASE