SMTL ID : 5d9i.1

SV40 Large T antigen origin binding domain bound to artificial DNA fork

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: V.22, N.81, L.93, I.94, C.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.93, A:C.95 Water bridges: A:V.22, A:V.77, A:Q.85 EDO.3: 4 residues within 4Å: Chain B: V.22, N.81, I.94, C.95 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.93, B:C.95 Water bridges: B:V.22, B:N.81

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 5 residues within 4Å: Chain B: K.39, A.84, Q.85, C.88, L.93 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.84, B:C.88, H2O.5 CA.4: 1 residues within 4Å: Chain D: G.22 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 2 residues within 4Å: Chain B: N.25 Chain D: G.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meinke, G. et al., Structure-based analysis of the interaction between the simian virus 40 T-antigen origin binding domain and single-stranded DNA. J. Virol. (2011)

Release Date

2015-09-09

Peptides

Large T antigen: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Large T antigen

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