SMTL ID : 9f74.1

Active SV40 LTAg complex with DNA (3D variability component_000, frame_015).

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

1 x DT- DT- DT- DT- DT- DT- DT- DT: Chains: S(Non-covalent)

DT-DT-DT-DT-DT-DT-DT-DT.1: 28 residues within 4Å: Chain A: F.194, K.246, K.247, H.248, L.249 Chain B: R.191, F.194, K.246, K.247, H.248 Chain C: R.191, F.194, K.246, K.247, H.248 Chain D: R.191, F.194, K.247, H.248 Chain E: R.191, F.194, K.246, K.247, H.248 Chain F: D.190, F.194, K.247, H.248 Protein-ligand interaction information (PLIP) not available

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 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 Chain B: K.153, R.275 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.164, A:S.165, A:S.165, A:S.165, A:G.166, A:K.167, A:T.168, A:T.168, A:T.168, A:T.169, A:T.169, A:N.264, A:K.285 Salt bridges: A:K.167, A:K.167, B:K.153, B:K.153, B:K.153, B:R.275 ATP.3: 25 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, D.209, N.264, R.283, P.284, K.285, D.286, L.288, K.289, L.292, L.299, I.304 Chain C: K.153, R.233, D.237, R.275 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:D.164, B:S.165, B:S.165, B:S.165, B:G.166, B:K.167, B:T.168, B:T.168, B:T.168, B:T.169, B:T.169, B:N.264, B:K.285, C:D.237 Salt bridges: B:K.167, B:K.167, C:K.153, C:K.153, C:K.153, C:R.275 ATP.4: 21 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, D.209, R.283, P.284, K.285, L.288, K.289, L.292, L.299, Q.305 Chain D: K.153, R.233 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.164, C:S.165, C:G.166, C:K.167, C:T.168, C:T.169, C:T.169, C:R.283, C:K.285 Salt bridges: C:K.167, C:K.167, D:R.233, D:R.233, D:R.233 ATP.5: 24 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, D.209, N.264, R.283, P.284, K.285, D.286, L.288, K.289, L.292, L.299, I.304, Q.305 Chain E: K.153, R.233 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:D.164, D:S.165, D:G.166, D:K.167, D:T.168, D:T.168, D:T.169, D:T.169, D:D.209, D:R.283, D:K.285, E:K.153, E:R.233 Salt bridges: D:K.167, D:K.167, E:R.233, E:R.233 ATP.6: 19 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 Chain F: R.233, S.239 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:D.164, E:S.165, E:G.166, E:K.167, E:T.168, E:T.168, E:T.168, E:T.169, E:T.169, E:N.264, E:R.283, E:K.285 Salt bridges: E:K.167, E:K.167, F:R.233 ATP.7: 21 residues within 4Å: Chain A: K.153 Chain F: W.128, L.132, P.162, I.163, D.164, S.165, G.166, K.167, T.168, T.169, K.211, N.264, R.283, P.284, K.285, L.288, K.289, L.292, L.299, Q.305 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:P.162, F:D.164, F:S.165, F:S.165, F:G.166, F:K.167, F:T.168, F:T.168, F:T.168, F:T.169, F:T.169, F:T.169, F:N.264, F:R.283, F:K.285 Salt bridges: F:K.167, F:K.167, F:K.211

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
A

B
B

C
C

D
D

E
E

F
F

Large T antigen

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