SMTL ID : 7un7.1

DNA Polymerase lambda in complex with a 1nt microhomology substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

1 x DC- DG- DG- DC- DA- DG- DT: DNA (5'-D(*CP*GP*GP*CP*AP*GP*T)-3')(Non-covalent)

DC-DG-DG-DC-DA-DG-DT.1: 18 residues within 4Å: Chain A: W.33, Y.259, R.268, R.271, A.272, K.275, L.281, S.282, E.283, R.292, H.295 Ligands: DC-DA-DG-DT-DA-DC.3, DC-DA-DG-DT-DA-DC.3, DG-DC-DC-DG.4, DG-DC-DC-DG.4, DG-DC-DC-DG.4, DG-DC-DC-DG.4, TTP.5 Protein-ligand interaction information (PLIP) not available

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

DT-DA-DC-DT-DG.2: 13 residues within 4Å: Chain A: Q.131, V.221, K.222, G.223, E.224, T.225, K.226, H.284 Ligands: DC-DA-DG-DT-DA-DC.3, DC-DA-DG-DT-DA-DC.3, DC-DA-DG-DT-DA-DC.3, DC-DA-DG-DT-DA-DC.3, DC-DA-DG-DT-DA-DC.3 Protein-ligand interaction information (PLIP) not available

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

DC-DA-DG-DT-DA-DC.3: 22 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, K.226, R.242, D.244, Y.259, F.260 Ligands: DC-DG-DG-DC-DA-DG-DT.1, DC-DG-DG-DC-DA-DG-DT.1, DT-DA-DC-DT-DG.2, DT-DA-DC-DT-DG.2, DT-DA-DC-DT-DG.2, DT-DA-DC-DT-DG.2, TTP.5, NA.7, CA.10 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.4: 18 residues within 4Å: Chain A: Y.26, W.33, R.34, G.37, Y.38, I.61, P.62, G.63, I.64, G.65, K.66, R.67, M.68, K.71 Ligands: DC-DG-DG-DC-DA-DG-DT.1, DC-DG-DG-DC-DA-DG-DT.1, DC-DG-DG-DC-DA-DG-DT.1, DC-DG-DG-DC-DA-DG-DT.1 Protein-ligand interaction information (PLIP) not available

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.5: 19 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, C.184, G.185, D.186, D.188, Y.259, F.260, T.261, G.262, S.263, A.264, N.267 Ligands: DC-DG-DG-DC-DA-DG-DT.1, DC-DA-DG-DT-DA-DC.3, CA.9, CA.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.264 Hydrogen bonds: A:S.176, A:S.176, A:S.176, A:R.179, A:G.185, A:D.186, A:N.267 Water bridges: A:Y.177, A:A.264 Salt bridges: A:R.145, A:R.179

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: M.110, Q.114 No protein-ligand interaction detected (PLIP)

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

NA.7: 4 residues within 4Å: Chain A: S.98, I.100, A.103 Ligands: DC-DA-DG-DT-DA-DC.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.102, A:A.103, A:A.103 NA.8: 2 residues within 4Å: Chain A: D.121, Q.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.121, A:Q.125

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: D.186, D.188 Ligands: TTP.5, CA.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.186, A:D.188, H2O.1 CA.10: 6 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DC.3, TTP.5, CA.9 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, A:D.244, H2O.1, H2O.2

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

EDO.11: 3 residues within 4Å: Chain A: E.89, Y.112, R.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.89, A:Y.112, A:R.117 EDO.12: 1 residues within 4Å: Chain A: P.92 No protein-ligand interaction detected (PLIP) EDO.13: 3 residues within 4Å: Chain A: R.123, L.128, A.133 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.133 EDO.14: 4 residues within 4Å: Chain A: N.99, W.101, F.142, L.143 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandramouly, G. et al., Pol lambda promotes microhomology-mediated end-joining. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-03-29

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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