SMTL ID : 6cst.1

Structure of human DNA polymerase kappa with DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x DA- DT- DA- DC- DA- DT- DA- DC- DC: DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3')(Non-covalent)

DA-DT-DA-DC-DA-DT-DA-DC-DC.1: 34 residues within 4Å: Chain A: Q.84, V.85, R.88, S.221, D.223, E.224, K.346, V.379, S.380, G.381, I.382, G.383, K.384, V.385, T.386, R.479, K.493, T.494, R.495, A.496, S.497, T.498 Chain C: G.5, G.6, T.7, A.8, T.9, G.10, T.11, A.12, T.13 Ligands: MG.4, EDO.20, DZ4.21 Protein-ligand interaction information (PLIP) not available DA-DT-DA-DC-DA-DT-DA-DC-DC.2: 33 residues within 4Å: Chain B: Q.84, V.85, S.221, D.223, E.224, K.346, V.379, S.380, G.381, I.382, G.383, K.384, V.385, T.386, R.479, K.493, T.494, R.495, A.496, S.497, T.498 Chain D: T.4, G.5, G.6, T.7, A.8, T.9, G.10, T.11, A.12, T.13 Ligands: MG.30, DZ4.36 Protein-ligand interaction information (PLIP) not available

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.132, M.133, D.223, K.353 Ligands: MG.4, DZ4.21 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.132, A:M.133, A:D.223 MG.4: 6 residues within 4Å: Chain A: D.132, D.223, E.224 Ligands: DA-DT-DA-DC-DA-DT-DA-DC-DC.1, MG.3, DZ4.21 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.132, A:D.223, A:E.224, H2O.4 MG.29: 6 residues within 4Å: Chain B: D.132, M.133, D.223, K.353 Ligands: MG.30, DZ4.36 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.132, B:M.133, B:D.223 MG.30: 6 residues within 4Å: Chain B: D.132, D.223, E.224 Ligands: DA-DT-DA-DC-DA-DT-DA-DC-DC.2, MG.29, DZ4.36 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.223, B:E.224

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: A.135, M.142, N.165, Y.166, H.167, P.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.166, A:H.167, A:H.167 PEG.6: 5 residues within 4Å: Chain A: H.418, Y.419, H.422, G.428, S.429 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.428 Water bridges: A:H.418 PEG.7: 4 residues within 4Å: Chain A: K.96, A.97, I.99 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.96 PEG.8: 5 residues within 4Å: Chain A: M.93, K.96, A.392, Q.404 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.96 PEG.31: 7 residues within 4Å: Chain B: D.134, A.135, M.142, N.165, Y.166, H.167, T.333 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.166, B:H.167, B:H.167, B:T.333

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: D.57, K.60 Ligand excluded by PLIP IOD.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.32: 1 residues within 4Å: Chain B: K.384 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain B: P.362, N.363 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain B: H.167 Ligand excluded by PLIP

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

EDO.12: 2 residues within 4Å: Chain A: E.454, Y.457 No protein-ligand interaction detected (PLIP) EDO.13: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.369 EDO.14: 4 residues within 4Å: Chain A: R.323, N.352, G.356, Q.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.323, A:N.352, A:Q.357 EDO.15: 2 residues within 4Å: Chain A: K.477, P.542 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.477 EDO.16: 3 residues within 4Å: Chain A: K.351, Y.358 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.351, A:Y.358 EDO.17: 4 residues within 4Å: Chain A: K.351, F.370, L.374 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.351 Water bridges: A:V.347 EDO.18: 4 residues within 4Å: Chain A: Q.461, A.506, E.507, F.510 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.461 EDO.19: 3 residues within 4Å: Chain A: P.375, I.396, T.397 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain A: R.43 Ligands: DA-DT-DA-DC-DA-DT-DA-DC-DC.1, DA-DT-DA-DC-DA-DT-DA-DC-DC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.43 EDO.35: 2 residues within 4Å: Chain B: E.454, Y.457 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.454, A:K.204

2 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.21: 19 residues within 4Å: Chain A: K.50, D.132, M.133, D.134, A.135, F.136, Y.137, S.162, T.163, Y.166, R.169, A.175, D.223, K.353 Chain C: T.4, G.5 Ligands: DA-DT-DA-DC-DA-DT-DA-DC-DC.1, MG.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.137 Hydrogen bonds: A:K.50, A:K.50, A:D.132, A:A.135, A:F.136, A:Y.137, A:T.163, A:T.163, A:R.169 Water bridges: A:K.50, A:D.132, A:Y.137, A:A.175 Salt bridges: A:K.50, A:R.169, A:K.353 DZ4.36: 18 residues within 4Å: Chain B: D.132, M.133, D.134, A.135, F.136, Y.137, S.162, T.163, Y.166, R.169, A.175, D.223, K.353 Chain D: T.4, G.5 Ligands: DA-DT-DA-DC-DA-DT-DA-DC-DC.2, MG.29, MG.30 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.137 Hydrogen bonds: B:D.132, B:A.135, B:F.136, B:Y.137, B:T.163, B:Y.166, B:Y.166, B:R.169 Water bridges: B:D.132, B:D.132, B:T.163, B:T.163 Salt bridges: B:R.169, B:K.353

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.22: 3 residues within 4Å: Chain A: N.352, K.353, P.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.352

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

CL.23: 2 residues within 4Å: Chain A: G.71, Y.75 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain A: L.529, L.531 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain A: N.195, D.197 Chain B: R.445 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: M.158 Chain D: T.1 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain A: M.44, M.177 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain B: I.65, M.177 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain A: S.458 Chain B: R.200, K.204 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain B: M.158 Chain C: T.1 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain B: K.207, S.221, L.222 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.28: 1 residues within 4Å: Chain A: N.489 No protein-ligand interaction detected (PLIP) K.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.42: 2 residues within 4Å: Chain B: N.487, N.489 No protein-ligand interaction detected (PLIP) K.43: 1 residues within 4Å: Chain C: C.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jha, V. et al., 2.0 angstrom resolution crystal structure of human pol kappa reveals a new catalytic function of N-clasp in DNA replication. Sci Rep (2018)

Release Date

2019-01-30

Peptides

DNA polymerase kappa: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA polymerase kappa

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