SMTL ID : 2py5.2 (1 other biounit)

Phi29 DNA polymerase complexed with single-stranded DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x DG- DG- DA- DC- DT- DT: 5'-d(GGACTTT)-3'(Non-covalent)

DG-DG-DA-DC-DT-DT.1: 16 residues within 4Å: Chain A: N.91, I.93, Y.101, M.102, Y.120, M.188, T.189, S.192, R.223, Y.226, G.391, K.392, A.394, S.395, N.396, K.422 Protein-ligand interaction information (PLIP) not available DG-DG-DA-DC-DT-DT.2: 17 residues within 4Å: Chain A: F.13, E.14, T.15, T.17, H.61, N.62, F.65, L.123, P.129, V.130, Y.148, Y.165, D.169, G.532, K.555, P.556, L.567 Protein-ligand interaction information (PLIP) not available

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

EDO.3: 4 residues within 4Å: Chain A: L.233, K.238, R.496, Q.497 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.233 EDO.4: 2 residues within 4Å: Chain A: S.260, R.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.261 Water bridges: A:S.260, A:S.260 EDO.5: 4 residues within 4Å: Chain A: I.474, L.480, G.481, Y.482 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.260, A:S.260, A:S.260, A:S.260, A:G.481 EDO.6: 5 residues within 4Å: Chain A: L.216, D.219, K.220, R.223, P.397 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.216, A:R.223, A:R.223 Water bridges: A:D.398 EDO.7: 4 residues within 4Å: Chain A: E.241, I.242, G.243, R.491 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.491 EDO.8: 5 residues within 4Å: Chain A: Y.259, I.364, D.365, T.368, L.480 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.364, A:D.365 EDO.9: 6 residues within 4Å: Chain A: H.485, E.486, S.487, T.488, E.515, G.516 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.486, A:T.488 Water bridges: A:H.485, A:T.488, A:E.515, A:G.516 EDO.10: 5 residues within 4Å: Chain A: E.33, D.34, H.35, L.178, K.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.35, A:H.35, A:K.182 EDO.11: 4 residues within 4Å: Chain A: V.528, K.529, C.530, K.538 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.530 Water bridges: A:M.533, A:M.533, A:K.538

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berman, A.J. et al., Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. Embo J. (2007)

Release Date

2007-07-17

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase

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