- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.64 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x DG- DA- DG- DA- DG- DT- DC- DA: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')(Non-covalent)
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 5 residues within 4Å:- Chain A: T.10, T.11
- Chain C: L.115
- Ligands: DG-DA-DG-DA-DG-DT-DC-DA.2, DG-DA-DG-DA-DG-DT-DC-DA.2
No protein-ligand interaction detected (PLIP)GOL.8: 5 residues within 4Å:- Chain B: T.10, T.11
- Chain D: L.115
- Ligands: DG-DA-DG-DA-DG-DT-DC-DA.1, DG-DA-DG-DA-DG-DT-DC-DA.1
No protein-ligand interaction detected (PLIP)GOL.11: 6 residues within 4Å:- Chain C: H.26, V.28, C.99, N.101, R.139
- Ligands: GOL.12
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.139
GOL.12: 5 residues within 4Å:- Chain C: H.26, E.42, N.101, R.103
- Ligands: GOL.11
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:H.26, C:N.101, C:N.101, C:R.103
- Water bridges: C:R.103
GOL.15: 5 residues within 4Å:- Chain D: H.26, V.28, C.99, N.101, R.139
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:R.139
- Water bridges: D:H.26, D:H.100, D:N.101
- 2 x MN: MANGANESE (II) ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
NA.5: 4 residues within 4Å:- Chain A: A.13
- Chain D: N.118
- Ligands: DG-DA-DG-DA-DG-DT-DC-DA.1, MN.4
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:H.97
- Water bridges: D:H.97
NA.7: 4 residues within 4Å:- Chain B: A.13
- Chain C: N.118
- Ligands: DG-DA-DG-DA-DG-DT-DC-DA.2, MN.6
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.118, C:N.118
- 4 x ZN: ZINC ION(Non-covalent)
ZN.9: 4 residues within 4Å:- Chain C: C.124, C.131, H.133, C.137
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:C.124, C:C.131, C:H.133, C:C.137
ZN.10: 4 residues within 4Å:- Chain C: C.40, C.99, C.104, H.109
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:C.40, C:C.99, C:C.104, C:H.109
ZN.13: 4 residues within 4Å:- Chain D: C.124, C.131, H.133, C.137
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:C.124, D:C.131, D:H.133, D:C.137
ZN.14: 4 residues within 4Å:- Chain D: C.40, C.99, C.104, H.109
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:C.40, D:C.99, D:C.104, D:H.109
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chang, C. et al., Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s. To Be Published
- Release Date
- 2024-07-10
- Peptides
- Intron-encoded endonuclease I-PpoI: CD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:C
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.64 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x DG- DA- DG- DA- DG- DT- DC- DA: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')(Non-covalent)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 2 x MN: MANGANESE (II) ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 4 x ZN: ZINC ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chang, C. et al., Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s. To Be Published
- Release Date
- 2024-07-10
- Peptides
- Intron-encoded endonuclease I-PpoI: CD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:C
AD
B