SMTL ID : 9evh.1

SV40 large T antigen assembly with DNA in presence of ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

1 x DT- DT- DT- DT- DT- DT- DT: DNA(Non-covalent)

DT-DT-DT-DT-DT-DT-DT.1: 23 residues within 4Å: Chain A: F.459, K.512, H.513, L.514 Chain B: R.456, F.459, K.512, H.513 Chain C: R.456, F.459, K.512, H.513 Chain D: R.456, F.459, K.512, H.513 Chain E: R.456, F.459, K.512, H.513 Chain F: F.459, K.512, H.513 Protein-ligand interaction information (PLIP) not available

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 20 residues within 4Å: Chain A: W.393, L.397, P.427, I.428, D.429, S.430, G.431, K.432, T.433, T.434, K.550, L.553, K.554, L.557, L.564, I.569, Q.570 Chain B: K.418, S.504, R.540 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.427, A:D.429, A:D.429, A:S.430, A:G.431, A:K.432, A:T.433, A:T.433, A:T.434, A:K.554, A:Q.570 Salt bridges: A:K.432, A:K.432, B:R.540 pi-Cation interactions: A:K.554 ADP.3: 20 residues within 4Å: Chain B: W.393, L.397, P.427, I.428, D.429, S.430, G.431, K.432, T.433, T.434, P.549, K.550, L.553, K.554, L.557, L.564, I.569 Chain C: K.418, S.504, R.540 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:P.427, B:D.429, B:D.429, B:S.430, B:G.431, B:G.431, B:K.432, B:T.433, B:T.433, B:T.434, B:T.434, B:K.550, B:K.550 Salt bridges: B:K.432, C:K.418, C:K.418 ADP.4: 19 residues within 4Å: Chain C: W.393, L.397, I.428, D.429, S.430, G.431, K.432, T.433, T.434, R.548, P.549, K.550, L.553, K.554, L.557, L.564, I.569 Chain D: K.418, R.498 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.429, C:D.429, C:S.430, C:G.431, C:T.433, C:T.433, C:T.434, C:T.434, C:R.548, C:K.550, D:K.418 Salt bridges: C:K.432, D:R.498 ADP.5: 21 residues within 4Å: Chain D: W.393, L.397, I.428, D.429, S.430, G.431, K.432, T.433, T.434, R.548, P.549, K.550, L.553, K.554, L.557, L.564, I.569, Q.570 Chain E: K.418, R.498, S.504 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:D.429, D:D.429, D:S.430, D:S.430, D:G.431, D:K.432, D:T.433, D:T.433, D:T.434, D:T.434, D:K.550 Salt bridges: D:K.432, E:R.498 ADP.6: 18 residues within 4Å: Chain E: W.393, L.397, I.428, D.429, S.430, G.431, K.432, T.433, T.434, R.548, P.549, K.550, L.553, K.554, L.557, L.564 Chain F: K.418, R.498 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:D.429, E:S.430, E:G.431, E:K.432, E:T.433, E:T.433, E:T.433, E:T.434, E:T.434, E:R.548, E:K.550 Salt bridges: E:K.432, F:R.498 ADP.7: 17 residues within 4Å: Chain F: W.393, L.397, I.428, D.429, S.430, G.431, K.432, T.433, T.434, R.548, P.549, K.550, D.551, L.553, K.554, L.557, L.564 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:P.427, F:D.429, F:S.430, F:G.431, F:K.432, F:T.433, F:T.433, F:T.434, F:R.548, F:K.550 Salt bridges: F:K.432

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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