SMTL ID : 5d46.1

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 2.80 Å

Oligo State

monomer

Ligands

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

DA-DA-DA-DA-DA-DC.1: 15 residues within 4Å: Chain A: T.176, Q.177, I.270, L.271, E.272, D.286, A.287, L.288, D.289, H.290 Ligands: DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2 Protein-ligand interaction information (PLIP) not available DA-DA-DA-DA-DA-DC.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-DC.3, DT-DT-DT-DT-DT-DG-DC.3, DT-DT-DT-DT-DT-DG-DC.3, DT-DT-DT-DT-DT-DG-DC.3, DT-DT-DT-DT-DT-DG-DC.3, ACT.10 Protein-ligand interaction information (PLIP) not available

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

DT-DT-DT-DT-DT-DG-DC.2: 32 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, A.287, L.288, F.295, R.322, D.324, G.339, W.340, T.341, 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-DC.3, DT-DT-DT-DT-DT-DG-DC.3, MG.5, NA.6, POP.7 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT-DT-DG-DC.3: 20 residues within 4Å: Chain A: L.79, R.83, D.286, A.287, R.344, E.347, R.348, R.351, R.352, T.355, H.356, L.362, D.363 Ligands: DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4 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-DC.2, POP.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.233, A:D.235

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-DC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.143, A:G.147, A:V.148

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.7: 10 residues within 4Å: Chain A: G.222, G.223, R.226, K.228, G.231, H.232, D.233, D.235 Ligands: DT-DT-DT-DT-DT-DG-DC.2, MG.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.223, A:H.232, A:D.233 Salt bridges: A:R.226, A:K.228, A:H.232

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

SO4.8: 4 residues within 4Å: Chain A: D.188, G.315, K.316, W.318 No protein-ligand interaction detected (PLIP) SO4.9: 1 residues within 4Å: Chain A: R.370 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.370

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

ACT.10: 5 residues within 4Å: Chain A: N.74, E.75, G.76, S.77 Ligands: DA-DA-DA-DA-DA-DC.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.76, A:S.77, A:S.77 Water bridges: A:E.75 ACT.11: 4 residues within 4Å: Chain A: L.51, K.228, M.229, T.230 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.51 Hydrogen bonds: A:M.229, A:T.230 Salt bridges: A:K.228 ACT.12: 1 residues within 4Å: Chain A: G.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.103 Water bridges: A:I.104

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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