SMTL ID : 9kak.1

CryoEM structure of LTag bound to SV40 AT half origin DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 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, D.209, N.264, R.283, P.284, K.285, L.288, K.289, L.292, L.299, I.304 Chain B: K.153, K.154, R.275 Ligands: MG.2 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:K.167, A:T.168, A:T.169, A:T.169, A:D.209, A:D.209, A:N.264, A:K.285, B:K.153, B:R.275, B:R.275 pi-Stacking: A:W.128 Salt bridges: B:K.153 ANP.4: 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, D.209, N.264, R.283, P.284, K.285, L.288, K.289, L.292, L.299, I.304 Chain C: K.153, K.154, R.275 Ligands: MG.3 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:P.162, B:D.164, B:S.165, B:S.165, B:G.166, B:K.167, B:K.167, B:T.168, B:T.168, B:T.169, B:T.169, B:D.209, 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: 22 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, R.233 Ligands: MG.5 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.164, C:S.165, C:S.165, C:G.166, C:K.167, C:K.167, C:T.168, C:T.169, C:T.169, C:N.264, C:K.285, D:K.153, D:R.233 ANP.8: 22 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, N.264, R.283, P.284, K.285, L.288, K.289, L.292, L.299, I.304 Chain E: K.153, R.233 Ligands: MG.7 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain E Hydrogen bonds: 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, E:R.233 Salt bridges: E:R.233 ANP.9: 20 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 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: 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:N.264, E:R.283, E:K.285 ANP.11: 26 residues within 4Å: Chain A: K.153, K.154, S.239, R.275 Chain F: W.128, L.132, P.162, I.163, D.164, S.165, G.166, K.167, T.168, T.169, E.208, N.264, R.283, P.284, K.285, L.288, K.289, L.292, L.299, I.304, Q.305 Ligands: MG.12 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:D.164, F:S.165, F:S.165, F:S.165, F:G.166, F:K.167, F:K.167, F:T.168, F:T.168, F:T.169, F:T.169, F:N.264, F:K.285, A:R.275, A:R.275

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.167, T.168, E.208, D.209 Chain B: R.275 Ligands: ANP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.168, A:D.209, A:D.209 MG.3: 6 residues within 4Å: Chain B: K.167, T.168, E.208, D.209 Chain C: R.275 Ligands: ANP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.168, B:D.209, B:D.209 MG.5: 2 residues within 4Å: Chain C: T.168 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.168 MG.7: 5 residues within 4Å: Chain D: K.167, T.168, E.208 Chain E: R.233 Ligands: ANP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.168 MG.10: 2 residues within 4Å: Chain E: T.168 Ligands: ANP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.168 MG.12: 4 residues within 4Å: Chain A: R.275 Chain F: T.168, E.208 Ligands: ANP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.168, F:E.208

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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