- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-hexamer
- Ligands
- 1 x DT- DT- DT- DT- DT- DT- DT: DNA(Non-covalent)
- 6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)
ANP.2: 24 residues within 4Å:- Chain A: W.128, L.132, P.162, I.163, D.164, S.165, G.166, K.167, T.168, T.169, N.264, R.283, P.284, K.285, D.286, L.288, K.289, L.292, L.299, I.304
- Chain B: P.152, K.153, R.275
- Ligands: MG.3
18 PLIP interactions:14 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:D.164, A:D.164, A:S.165, A:S.165, A:G.166, A:K.167, A:K.167, A:T.168, A:T.169, A:T.169, A:N.264, A:R.283, A:K.285, B:K.153, B:R.275, B:R.275
- pi-Stacking: A:W.128
- Salt bridges: B:K.153
ANP.5: 24 residues within 4Å:- Chain B: W.128, L.132, P.162, I.163, D.164, S.165, G.166, K.167, T.168, T.169, N.264, R.283, P.284, K.285, D.286, L.288, K.289, L.292, L.299, I.304
- Chain C: K.153, K.154, R.275
- Ligands: MG.4
20 PLIP interactions:16 interactions with chain B, 4 interactions with chain C- Hydrogen bonds: B:P.162, B:D.164, B:D.164, B:D.164, B:S.165, B:S.165, B:G.166, B:K.167, B:K.167, B:T.168, B:T.169, B:T.169, B:N.264, B:R.283, B:K.285, C:K.153, C:R.275, C:R.275
- pi-Stacking: B:W.128
- Salt bridges: C:K.153
ANP.6: 23 residues within 4Å:- Chain C: W.128, L.132, P.162, I.163, D.164, S.165, G.166, K.167, T.168, T.169, N.264, R.283, P.284, K.285, L.288, K.289, L.292, L.299, I.304
- Chain D: K.153, K.154, R.275
- Ligands: MG.7
16 PLIP interactions:14 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:P.162, C:D.164, C:D.164, C:D.164, C:S.165, C:G.166, C:K.167, C:K.167, C:T.168, C:T.169, C:T.169, C:R.283, C:K.285, D:R.275, D:R.275
- pi-Stacking: C:W.128
ANP.8: 21 residues within 4Å:- Chain D: W.128, L.132, P.162, I.163, D.164, S.165, G.166, K.167, T.168, T.169, R.283, P.284, K.285, L.288, K.289, L.292, L.299, I.304
- Chain E: K.153, R.233
- Ligands: MG.9
15 PLIP interactions:14 interactions with chain D, 1 interactions with chain E- Hydrogen bonds: D:P.162, D:D.164, D:D.164, D:S.165, D:S.165, D:G.166, D:K.167, D:K.167, D:T.168, D:T.169, D:T.169, D:K.285, E:K.153
- pi-Stacking: D:W.128, D:W.128
ANP.10: 23 residues within 4Å:- Chain E: W.128, L.132, P.162, I.163, D.164, S.165, G.166, K.167, T.168, T.169, N.264, R.283, P.284, K.285, L.288, K.289, L.292, L.299, I.304, Q.305
- Chain F: K.153, R.233
- Ligands: MG.11
13 PLIP interactions:2 interactions with chain F, 11 interactions with chain E- Hydrogen bonds: F:K.153, F:R.233, E:P.162, E:D.164, E:S.165, E:G.166, E:K.167, E:K.167, E:T.168, E:T.169, E:T.169, E:R.283, E:K.285
ANP.12: 19 residues within 4Å:- Chain F: W.128, L.132, P.162, I.163, D.164, S.165, G.166, K.167, T.168, T.169, N.264, P.284, K.285, L.288, K.289, L.292, I.304, Q.305
- Ligands: MG.13
12 PLIP interactions:12 interactions with chain F- Hydrogen bonds: F:P.162, F:D.164, F:S.165, F:G.166, F:K.167, F:K.167, F:T.168, F:T.169, F:T.169, F:K.285, F:K.285, F:K.289
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 4 residues within 4Å:- Chain A: K.167, T.168
- Chain B: R.275
- Ligands: ANP.2
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:T.168
MG.4: 5 residues within 4Å:- Chain B: K.167, T.168, E.208
- Chain C: R.275
- Ligands: ANP.5
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:T.168
MG.7: 4 residues within 4Å:- Chain C: K.167, T.168
- Chain D: R.275
- Ligands: ANP.6
1 PLIP interactions:1 interactions with chain C- Metal complexes: C:T.168
MG.9: 3 residues within 4Å:- Chain D: K.167, T.168
- Ligands: ANP.8
1 PLIP interactions:1 interactions with chain D- Metal complexes: D:T.168
MG.11: 2 residues within 4Å:- Chain E: T.168
- Ligands: ANP.10
1 PLIP interactions:1 interactions with chain E- Metal complexes: E:T.168
MG.13: 3 residues within 4Å:- Chain F: K.167, T.168
- Ligands: ANP.12
1 PLIP interactions:1 interactions with chain F- Metal complexes: F:T.168
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shahid, T. et al., Structural dynamics of DNA unwinding by a replicative helicase. Nature (2025)
- Release Date
- 2025-02-05
- Peptides
- Large T antigen: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-hexamer
- Ligands
- 1 x DT- DT- DT- DT- DT- DT- DT: DNA(Non-covalent)
- 6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shahid, T. et al., Structural dynamics of DNA unwinding by a replicative helicase. Nature (2025)
- Release Date
- 2025-02-05
- Peptides
- Large T antigen: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F