SMTL ID : 7m09.1

Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate and incoming dUMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x DC- DG- DG- DC- DA: DNA (5'-D(*CP*GP*GP*CP*A)-3')(Non-covalent)

DC-DG-DG-DC-DA.1: 12 residues within 4Å: Chain A: W.45, L.48, R.285, R.288, K.292 Ligands: DC-DA-DG-DT-DG-DC.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DA-DC-DT-DG.4, DUP.5 Protein-ligand interaction information (PLIP) not available

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

DC-DA-DG-DT-DG-DC.2: 27 residues within 4Å: Chain A: I.112, W.113, G.114, A.115, G.116, T.117, K.118, T.119, D.200, K.243, L.245, R.259, D.261, Y.276, F.277 Ligands: DC-DG-DG-DC-DA.1, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DUP.5, CA.6, MG.7, NA.9, GOL.15 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: DNA (5'-D(P*GP*CP*CP*G)-3')(Non-covalent)

DG-DC-DC-DG.3: 19 residues within 4Å: Chain A: Y.38, W.45, R.46, G.49, Y.50, I.73, P.74, G.75, I.76, G.77, K.78, R.79, M.80, K.83 Ligands: DC-DG-DG-DC-DA.1, DC-DG-DG-DC-DA.1, DC-DG-DG-DC-DA.1, DC-DG-DG-DC-DA.1, NA.10 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DA- DC- DT- DG: DNA (5'-D(*GP*CP*AP*CP*TP*G)-3')(Non-covalent)

DG-DC-DA-DC-DT-DG.4: 20 residues within 4Å: Chain A: V.233, Q.235, Q.241, Q.242, K.243, Y.276, R.288, S.297, L.298, S.299, E.300, H.301 Ligands: DC-DG-DG-DC-DA.1, DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, GOL.15 Protein-ligand interaction information (PLIP) not available

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.5: 21 residues within 4Å: Chain A: R.157, G.187, S.188, R.191, C.196, G.197, D.198, D.200, Y.276, F.277, T.278, G.279, S.280, A.281, N.284 Ligands: DC-DG-DG-DC-DA.1, DC-DA-DG-DT-DG-DC.2, CA.6, MG.7, MG.8, NA.13 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.281 Hydrogen bonds: A:S.188, A:S.188, A:S.188, A:R.191, A:R.191, A:G.197, A:D.198, A:D.198, A:N.284 Water bridges: A:R.157, A:R.157, A:R.157, A:A.281 Salt bridges: A:R.157

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 7 residues within 4Å: Chain A: D.198, D.200, D.261 Ligands: DC-DA-DG-DT-DG-DC.2, DUP.5, MG.7, MG.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.200, A:D.261, H2O.3

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 7 residues within 4Å: Chain A: D.198, D.200, D.261 Ligands: DC-DA-DG-DT-DG-DC.2, DUP.5, CA.6, MG.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.200, A:D.261, H2O.3 MG.8: 5 residues within 4Å: Chain A: D.198, D.200 Ligands: DUP.5, CA.6, MG.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.200, H2O.5

3 x NA: SODIUM ION(Non-functional Binders)

NA.9: 5 residues within 4Å: Chain A: S.110, I.112, G.114, A.115 Ligands: DC-DA-DG-DT-DG-DC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.114, A:A.115, A:A.115 NA.10: 4 residues within 4Å: Chain A: C.71, I.73, I.76 Ligands: DG-DC-DC-DG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.73, A:I.76 NA.13: 1 residues within 4Å: Ligands: DUP.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.157

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

CL.11: 3 residues within 4Å: Chain A: Q.41, I.99, S.100 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: T.326, E.327 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 5 residues within 4Å: Chain A: R.223, L.228, T.229, D.230, D.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.223, A:D.231 Water bridges: A:D.231 GOL.15: 10 residues within 4Å: Chain A: W.113, V.233, K.243, L.245 Ligands: DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.243 Water bridges: A:Q.143, A:Q.143, A:Q.143, A:K.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaminski, A.M. et al., Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining. Nat Commun (2022)

Release Date

2022-03-16

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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