SMTL ID : 2py5.1 (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

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

DG-DA-DC-DT-DT-DT.1: 21 residues within 4Å: Chain A: F.13, E.14, T.15, T.17, H.61, N.62, F.65, Q.99, L.123, P.129, V.130, Y.148, D.169, N.313, L.567 Ligands: DG-DG-DA-DC-DT-DT.2, DG-DG-DA-DC-DT-DT.2, DG-DG-DA-DC-DT-DT.2, DG-DG-DA-DC-DT-DT.2, DG-DG-DA-DC-DT-DT.3, DG-DG-DA-DC-DT-DT.3 Protein-ligand interaction information (PLIP) not available DG-DA-DC-DT-DT-DT.2: 16 residues within 4Å: Chain A: K.64, I.94, M.97, G.98, W.100, N.313, K.402, K.407, F.414, A.531, G.532, Q.560 Ligands: DG-DA-DC-DT-DT-DT.1, DG-DA-DC-DT-DT-DT.1, DG-DA-DC-DT-DT-DT.1, DG-DG-DA-DC-DT-DT.3 Protein-ligand interaction information (PLIP) not available DG-DA-DC-DT-DT-DT.3: 22 residues within 4Å: Chain A: N.91, I.93, M.97, Q.99, Y.101, M.102, Y.120, M.188, T.189, S.192, R.223, G.391, K.392, A.394, S.395, N.396, V.399, K.422 Ligands: DG-DA-DC-DT-DT-DT.1, DG-DA-DC-DT-DT-DT.1, DG-DG-DA-DC-DT-DT.2, DG-DG-DA-DC-DT-DT.2 Protein-ligand interaction information (PLIP) not available

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

EDO.4: 5 residues within 4Å: Chain A: S.252, K.371, K.383, L.386, N.387 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: S.260, L.262, T.357 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: L.294, K.295, E.296, G.297, Y.298, K.317, Y.449 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: N.234, R.236, Y.449 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: K.490, R.491 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.208, F.211, P.212, T.213 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: Y.259, I.364, D.365, T.368, L.480 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: Y.405, R.415 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: S.43, D.45 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: K.206, V.210, Y.265, T.356 Ligands: EDO.14 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: K.206, T.356, T.357, G.358, L.359 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: E.334, W.436, Y.439 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: A.256, Q.257, S.260, R.261, T.440, G.481 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: D.456, T.457, D.458, S.459 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: I.269, D.278, Y.281, K.352 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: H.485, E.486, S.487, G.516 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: E.338, T.443, Q.446, A.447 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: I.504, E.515, K.525 Ligand excluded by PLIP

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
A

DNA polymerase

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