SMTL ID : 4k8x.1

Binary complex of 9N DNA polymerase in the replicative state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: R.406, S.407, R.460, K.487 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.406, A:R.460, A:K.487 SO4.2: 2 residues within 4Å: Chain A: Y.30, R.32 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.32 SO4.3: 2 residues within 4Å: Chain A: R.484 Chain B: A.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.484 SO4.4: 5 residues within 4Å: Chain A: K.360, K.363, R.364, L.452, D.455 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.360, A:K.363, A:R.364 SO4.5: 4 residues within 4Å: Chain A: Y.388, V.389, K.390, E.391 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.388, A:Y.388, A:E.391 SO4.6: 4 residues within 4Å: Chain A: E.130, G.131, R.335, R.482 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.131 Salt bridges: A:R.335, A:R.482 SO4.7: 2 residues within 4Å: Chain A: R.97, D.113 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.97 SO4.8: 6 residues within 4Å: Chain A: T.136, M.137, D.164, G.165, Y.320, R.324 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.137, A:G.165, A:Y.320, A:Y.320 Salt bridges: A:R.324 SO4.9: 3 residues within 4Å: Chain A: K.289, Y.291, A.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.292 Salt bridges: A:K.289 SO4.11: 4 residues within 4Å: Chain A: R.406, S.407, K.487, N.491 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.407, A:N.491 Water bridges: A:L.408 Salt bridges: A:K.487 SO4.12: 5 residues within 4Å: Chain A: Y.7, P.90, Q.91, P.115, F.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.116

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain A: Y.110, P.369, N.370 Ligand excluded by PLIP

1 x 5CY: 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium(Non-covalent)

5CY.13: 7 residues within 4Å: Chain A: T.267, I.268, V.282, F.283, E.325, F.326 Chain B: A.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.267, A:I.268, A:F.283, A:E.325 pi-Stacking: A:F.326

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

EDO.14: 2 residues within 4Å: Chain A: G.245 Chain B: G.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bergen, K. et al., Structures of KOD and 9N DNA Polymerases Complexed with Primer Template Duplex. Chembiochem (2013)

Release Date

2013-06-26

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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