SMTL ID : 7m0e.1 (3 other biounits)

Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and incoming dUMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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.47, L.50, N.240, Y.278, R.287, R.290, A.291, K.294, L.300, S.301, E.302, H.303 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, DUP.4 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: 20 residues within 4Å: Chain A: I.114, W.115, G.116, A.117, G.118, T.119, K.120, T.121, D.202, R.261, D.263, Y.278, F.279 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, DUP.4, NA.6, MG.8, SO4.9 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: 17 residues within 4Å: Chain A: Y.40, W.47, R.48, G.51, Y.52, P.76, G.77, I.78, G.79, K.80, R.81, M.82, K.85 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 Protein-ligand interaction information (PLIP) not available

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

DUP.4: 17 residues within 4Å: Chain A: R.159, G.189, S.190, R.193, C.198, G.199, D.200, D.202, Y.278, F.279, T.280, G.281, A.283, N.286 Ligands: DC-DG-DG-DC-DA-DG-DC.1, DC-DA-DG-DT-DG-DC.2, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.283 Hydrogen bonds: A:S.190, A:S.190, A:S.190, A:R.193, A:R.193, A:G.199, A:D.200, A:D.200, A:N.286 Water bridges: A:R.261, A:R.261, A:A.283 Salt bridges: A:R.159

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 3 residues within 4Å: Chain A: D.200, D.202 Ligands: DUP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.200, A:D.202, H2O.2 MG.8: 2 residues within 4Å: Ligands: DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2 No protein-ligand interaction detected (PLIP)

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

NA.6: 5 residues within 4Å: Chain A: S.112, I.114, G.116, A.117 Ligands: DC-DA-DG-DT-DG-DC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.116, A:A.117, A:A.117

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

EDO.7: 3 residues within 4Å: Chain A: E.167, T.171, L.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.167, A:E.167

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

SO4.9: 3 residues within 4Å: Chain A: Q.145 Ligands: DC-DA-DG-DT-DG-DC.2, DC-DA-DG-DT-DG-DC.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.145

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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