SMTL ID : 5d49.1

Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

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

DA-DA-DA-DA-DA-DC.1: 15 residues within 4Å: Chain A: R.174, T.176, Q.177, D.269, I.270, L.271, E.272, T.274, D.286 Ligands: DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2 Protein-ligand interaction information (PLIP) not available

2 x DT- DT- DT- DT- DT- DG- DG- DC: DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3')(Non-covalent)

DT-DT-DT-DT-DT-DG-DG-DC.2: 33 residues within 4Å: Chain A: V.145, F.146, G.147, V.148, G.149, L.150, K.151, T.152, M.178, D.233, D.235, L.271, D.286, A.287, L.288, F.295, R.322, D.324, G.339, W.340, G.342, R.344, E.347 Ligands: DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DT-DT-DT-DT-DT-DG-DG-DC.3, DT-DT-DT-DT-DT-DG-DG-DC.3, MG.5, NA.6, SO4.7 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT-DT-DG-DG-DC.3: 20 residues within 4Å: Chain A: G.76, L.79, R.83, R.283, A.287, R.344, E.347, R.348, R.351, R.352, T.355, H.356, M.361 Ligands: DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2, DA-DA-DA-DA-DA.4, DA-DA-DA-DA-DA.4, DA-DA-DA-DA-DA.4, DA-DA-DA-DA-DA.4, DA-DA-DA-DA-DA.4 Protein-ligand interaction information (PLIP) not available

1 x DA- DA- DA- DA- DA: DNA (5'-D(*AP*AP*AP*AP*A)-3')(Non-covalent)

DA-DA-DA-DA-DA.4: 18 residues within 4Å: Chain A: Q.42, G.76, S.77, A.80, F.81, P.105, C.106, L.107, G.108, D.109, K.110, V.111 Ligands: DT-DT-DT-DT-DT-DG-DG-DC.3, DT-DT-DT-DT-DT-DG-DG-DC.3, DT-DT-DT-DT-DT-DG-DG-DC.3, DT-DT-DT-DT-DT-DG-DG-DC.3, DT-DT-DT-DT-DT-DG-DG-DC.3, ACT.9 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.233, D.235 Ligands: DT-DT-DT-DT-DT-DG-DG-DC.2, SO4.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, H2O.1, H2O.6

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

NA.6: 5 residues within 4Å: Chain A: T.143, V.145, G.147, V.148 Ligands: DT-DT-DT-DT-DT-DG-DG-DC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.143, A:G.147, A:V.148

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

SO4.7: 6 residues within 4Å: Chain A: G.222, G.223, R.226, D.235 Ligands: DT-DT-DT-DT-DT-DG-DG-DC.2, MG.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.223 Water bridges: A:R.226, A:R.226, A:K.228, A:H.232 Salt bridges: A:R.226 SO4.8: 4 residues within 4Å: Chain A: D.188, E.314, G.315, K.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.316 Water bridges: A:K.316 Salt bridges: A:K.316

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 5 residues within 4Å: Chain A: N.74, E.75, G.76, S.77 Ligands: DA-DA-DA-DA-DA.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.74 Hydrogen bonds: A:G.76, A:S.77, A:S.77 Water bridges: A:E.75, A:S.77 ACT.10: 3 residues within 4Å: Chain A: K.228, M.229, T.230 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.229, A:T.230 Hydrogen bonds: A:M.229, A:T.230, A:T.230 Salt bridges: A:K.228 ACT.11: 3 residues within 4Å: Chain A: E.102, G.103, K.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.103 Water bridges: A:I.104, A:K.112 Salt bridges: A:K.112

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 5 residues within 4Å: Chain A: L.213, P.214, D.215, E.242, E.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.215, A:E.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loc'h, J. et al., Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination. Structure (2016)

Release Date

2016-07-27

Peptides

Terminal deoxynucleotidyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Terminal deoxynucleotidyltransferase

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