SMTL ID : 7m0d.1 (1 other biounit)

Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB substrate and incoming dUMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

DC-DG-DG-DC-DA-DG-DC.1: 19 residues within 4Å: Chain A: W.45, Y.276, R.285, R.288, A.289, K.292, L.298, S.299, E.300, H.301, K.315 Ligands: DC-DA-DG-DT-DG-DC.2, 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, 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: 25 residues within 4Å: Chain A: I.112, W.113, G.114, A.115, G.116, T.117, K.118, T.119, L.245, R.259, D.261, Y.276, F.277 Ligands: DC-DG-DG-DC-DA-DG-DC.1, DC-DG-DG-DC-DA-DG-DC.1, DC-DG-DG-DC-DA-DG-DC.1, DA-DC-DT-DG.4, DA-DC-DT-DG.4, DA-DC-DT-DG.4, DA-DC-DT-DG.4, DUP.5, NA.6, NA.8, TRS.13, EDO.19 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, P.74, G.75, I.76, G.77, K.78, R.79, M.80, K.83, K.95 Ligands: DC-DG-DG-DC-DA-DG-DC.1, DC-DG-DG-DC-DA-DG-DC.1, DC-DG-DG-DC-DA-DG-DC.1, DC-DG-DG-DC-DA-DG-DC.1, K.9 Protein-ligand interaction information (PLIP) not available

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

DA-DC-DT-DG.4: 12 residues within 4Å: Chain A: T.142, Q.143, V.233, S.234, Q.235, N.238 Ligands: DC-DG-DG-DC-DA-DG-DC.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 Protein-ligand interaction information (PLIP) not available

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

DUP.5: 19 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, A.281, N.284 Ligands: DC-DG-DG-DC-DA-DG-DC.1, DC-DA-DG-DT-DG-DC.2, NA.6, MG.7, TRS.13 14 PLIP interactions: 14 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:N.284 Water bridges: A:R.157, A:R.157, A:R.157, A:A.281 Salt bridges: A:R.157

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

NA.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, TRS.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.261 NA.8: 6 residues within 4Å: Chain A: S.110, I.112, A.115 Ligands: DC-DA-DG-DT-DG-DC.2, K.10, EDO.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.112, A:G.114, A:A.115

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: D.198, D.200 Ligands: DUP.5, NA.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.200, H2O.2

3 x K: POTASSIUM ION(Non-covalent)

K.9: 4 residues within 4Å: Chain A: C.71, I.73, I.76 Ligands: DG-DC-DC-DG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.71, A:I.73, A:I.76, H2O.12, H2O.20 K.10: 3 residues within 4Å: Chain A: S.110 Ligands: NA.8, EDO.19 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.110, H2O.8, H2O.19 K.11: 6 residues within 4Å: Chain A: Q.18, T.21, H.23, K.58, S.59, F.60 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.18, A:T.21, A:K.58, A:F.60, H2O.13

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 7 residues within 4Å: Chain A: E.167, Q.168, Q.171, C.183, V.184, A.185 Ligands: EDO.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.168, A:Q.171, A:Q.171, A:A.185 Water bridges: A:E.167, A:C.183, A:A.185 TRS.13: 8 residues within 4Å: Chain A: W.113, D.198, R.259 Ligands: DC-DA-DG-DT-DG-DC.2, DUP.5, NA.6, EDO.18, EDO.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.198, A:R.259 Water bridges: A:R.157

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.14: 3 residues within 4Å: Chain A: L.182, Y.267 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.182 Water bridges: A:Y.267

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

EDO.15: 3 residues within 4Å: Chain A: Q.168, Q.171 Ligands: TRS.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.168, A:Q.168, A:Q.171 Water bridges: A:Q.175, A:Q.175 EDO.16: 5 residues within 4Å: Chain A: L.274, P.325, T.326, E.327 Ligands: CIT.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.327 Water bridges: A:E.327, A:K.328, A:K.328 EDO.17: 3 residues within 4Å: Chain A: G.127, R.129, D.133 No protein-ligand interaction detected (PLIP) EDO.18: 6 residues within 4Å: Chain A: N.111, I.112, W.113, F.154 Ligands: TRS.13, EDO.19 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.113 EDO.19: 9 residues within 4Å: Chain A: S.110, I.112, W.113 Ligands: DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2, NA.8, K.10, TRS.13, EDO.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.112

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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