SMTL ID : 7m07.1

Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

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.1: 24 residues within 4Å: Chain A: I.112, W.113, G.114, A.115, G.116, T.117, K.118, T.119, D.200, L.245, R.259, D.261, Y.276, F.277 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: DUP.3, MG.4, NA.6 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.2: 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 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.7 Protein-ligand interaction information (PLIP) not available

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

DUP.3: 18 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 Chain B: A.5 Ligands: DC-DA-DG-DT-DA-DC.1, MG.4, MG.5 12 PLIP interactions: 12 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:A.281 Salt bridges: A:R.157

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

NA.6: 5 residues within 4Å: Chain A: S.110, I.112, W.113, A.115 Ligands: DC-DA-DG-DT-DA-DC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.114, A:A.115, A:A.115 NA.7: 4 residues within 4Å: Chain A: C.71, I.73, I.76 Ligands: DG-DC-DC-DG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.73 NA.8: 5 residues within 4Å: Chain A: Q.18, T.21, K.58, S.59, F.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.60 Water bridges: A:H.23 NA.10: 2 residues within 4Å: Chain A: S.234 Chain B: T.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.234 Water bridges: A:E.236 NA.15: 2 residues within 4Å: Chain B: G.3, C.4 No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain A: Q.41, I.99, S.100 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: T.326, E.327 Ligand excluded by PLIP

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

EDO.12: 5 residues within 4Å: Chain A: R.223, L.228, T.229, D.230, D.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.223, A:D.231 EDO.13: 4 residues within 4Å: Chain A: Q.242, I.263, V.265, H.301 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.243, A:H.301 EDO.14: 2 residues within 4Å: Chain A: E.156, R.256 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.156 Water bridges: A:E.156, A:E.156, A:R.256, A:R.256

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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