- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x DT- DG- DC- DG: DNA (5'-D(*TP*GP*CP*G)-3')(Non-covalent)
- 4 x DC- DC- DG- DG- DC- DG- DC: DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')(Non-covalent)
DC-DC-DG-DG-DC-DG-DC.2: 35 residues within 4Å:- Chain A: P.61, Q.63, T.64, N.67, R.100, R.191, D.193
- Chain B: S.31, D.34, S.36, R.59, G.62, Q.63, S.65, G.66, D.140, K.187, W.188, T.189, R.191, R.194, N.197, R.227
- Ligands: DT-DG-DC-DG.1, DT-DG-DC-DG.3, DT-DG-DC-DG.3, DT-DG-DC-DG.3, DT-DG-DC-DG.3, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4, MG.9, MG.15, ACY.16
Protein-ligand interaction information (PLIP) not availableDC-DC-DG-DG-DC-DG-DC.4: 34 residues within 4Å:- Chain A: S.31, D.34, S.36, R.59, G.62, Q.63, S.65, G.66, D.140, K.187, W.188, T.189, R.191, R.194, N.197, R.227
- Chain B: P.61, Q.63, T.64, N.67, R.191, D.193
- Ligands: DT-DG-DC-DG.1, DT-DG-DC-DG.1, DT-DG-DC-DG.1, DT-DG-DC-DG.1, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DT-DG-DC-DG.3, MG.10, MG.13, ACY.14
Protein-ligand interaction information (PLIP) not availableDC-DC-DG-DG-DC-DG-DC.6: 34 residues within 4Å:- Chain C: S.31, D.34, S.36, R.59, G.62, Q.63, S.65, G.66, D.140, K.187, W.188, T.189, R.191, R.194, N.197, R.227
- Chain D: P.61, Q.63, T.64, N.67, R.191, D.193
- Ligands: DT-DG-DC-DG.5, DT-DG-DC-DG.7, DT-DG-DC-DG.7, DT-DG-DC-DG.7, DT-DG-DC-DG.7, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8, MG.11, MG.17, ACY.18
Protein-ligand interaction information (PLIP) not availableDC-DC-DG-DG-DC-DG-DC.8: 35 residues within 4Å:- Chain C: P.61, Q.63, T.64, N.67, R.191, D.193
- Chain D: S.31, D.34, S.36, R.59, G.62, Q.63, S.65, G.66, E.70, D.140, K.187, W.188, T.189, R.191, R.194, N.197, R.227
- Ligands: DT-DG-DC-DG.5, DT-DG-DC-DG.5, DT-DG-DC-DG.5, DT-DG-DC-DG.5, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DT-DG-DC-DG.7, MG.12, MG.19, ACY.20
Protein-ligand interaction information (PLIP) not available- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.9: 4 residues within 4Å:- Chain B: D.140
- Ligands: DC-DC-DG-DG-DC-DG-DC.2, MG.15, ACY.16
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:D.140, H2O.26, H2O.463, H2O.521
MG.10: 4 residues within 4Å:- Chain A: D.140
- Ligands: DC-DC-DG-DG-DC-DG-DC.4, MG.13, ACY.14
4 PLIP interactions:1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:D.140, H2O.52, H2O.200, H2O.231
MG.11: 4 residues within 4Å:- Chain C: D.140
- Ligands: DC-DC-DG-DG-DC-DG-DC.6, MG.17, ACY.18
4 PLIP interactions:1 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:D.140, H2O.115, H2O.726, H2O.727
MG.12: 4 residues within 4Å:- Chain D: D.140
- Ligands: DC-DC-DG-DG-DC-DG-DC.8, MG.19, ACY.20
4 PLIP interactions:1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:D.140, H2O.1003, H2O.1086, H2O.1095
MG.13: 5 residues within 4Å:- Chain A: D.140, C.186
- Ligands: DC-DC-DG-DG-DC-DG-DC.4, MG.10, ACY.14
5 PLIP interactions:2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions- Metal complexes: A:D.140, A:C.186, ACY.14, H2O.65, H2O.202
MG.15: 5 residues within 4Å:- Chain B: D.140, C.186
- Ligands: DC-DC-DG-DG-DC-DG-DC.2, MG.9, ACY.16
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.140, B:C.186, H2O.20, H2O.508
MG.17: 5 residues within 4Å:- Chain C: D.140, C.186
- Ligands: DC-DC-DG-DG-DC-DG-DC.6, MG.11, ACY.18
5 PLIP interactions:2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions- Metal complexes: C:D.140, C:C.186, ACY.18, H2O.121, H2O.728
MG.19: 5 residues within 4Å:- Chain D: D.140, C.186
- Ligands: DC-DC-DG-DG-DC-DG-DC.8, MG.12, ACY.20
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.140, D:C.186, H2O.164, H2O.999
- 4 x ACY: ACETIC ACID(Non-functional Binders)
ACY.14: 10 residues within 4Å:- Chain A: D.140, S.185, C.186, K.187, N.197, A.198, E.201
- Ligands: DC-DC-DG-DG-DC-DG-DC.4, MG.10, MG.13
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:A.198
- Hydrogen bonds: A:C.186
- Water bridges: A:K.187, A:N.197
- Salt bridges: A:K.187
ACY.16: 10 residues within 4Å:- Chain B: D.140, S.185, C.186, K.187, N.197, A.198, E.201
- Ligands: DC-DC-DG-DG-DC-DG-DC.2, MG.9, MG.15
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:A.198
- Hydrogen bonds: B:C.186
- Water bridges: B:K.187
- Salt bridges: B:K.187
ACY.18: 10 residues within 4Å:- Chain C: D.140, S.185, C.186, K.187, N.197, A.198, E.201
- Ligands: DC-DC-DG-DG-DC-DG-DC.6, MG.11, MG.17
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:A.198
- Hydrogen bonds: C:C.186, C:E.201
- Water bridges: C:K.187
- Salt bridges: C:K.187
ACY.20: 10 residues within 4Å:- Chain D: D.140, S.185, C.186, K.187, N.197, A.198, E.201
- Ligands: DC-DC-DG-DG-DC-DG-DC.8, MG.12, MG.19
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:A.198
- Hydrogen bonds: D:C.186
- Water bridges: D:D.140, D:K.187
- Salt bridges: D:K.187
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Deibert, M. et al., Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat.Struct.Biol. (2000)
- Release Date
- 2001-02-07
- Peptides
- TYPE II RESTRICTION ENZYME NGOMI: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x DT- DG- DC- DG: DNA (5'-D(*TP*GP*CP*G)-3')(Non-covalent)
- 4 x DC- DC- DG- DG- DC- DG- DC: DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 4 x ACY: ACETIC ACID(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Deibert, M. et al., Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat.Struct.Biol. (2000)
- Release Date
- 2001-02-07
- Peptides
- TYPE II RESTRICTION ENZYME NGOMI: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D