SMTL ID : 5d4b.1 (1 other biounit)

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 2.66 Å

Oligo State

monomer

Ligands

2 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: 25 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.288, F.295, R.322, D.324, G.339, W.340, T.341, G.342, R.344, E.347 Ligands: MG.4, NA.5, SO4.8, SO4.9 Protein-ligand interaction information (PLIP) not available DA-DA-DA-DA-DA-DC.2: 12 residues within 4Å: Chain A: G.76, L.79, R.83, R.283, R.352, T.355, H.356 Ligands: DT-DT-DT-DT-DT-DG-DG.3, DT-DT-DT-DT-DT-DG-DG.3, DT-DT-DT-DT-DT-DG-DG.3, DT-DT-DT-DT-DT-DG-DG.3, DT-DT-DT-DT-DT-DG-DG.3 Protein-ligand interaction information (PLIP) not available

1 x DT- DT- DT- DT- DT- DG- DG: DNA (5'-D(*TP*TP*TP*TP*TP*GP*G)-3')(Non-covalent)

DT-DT-DT-DT-DT-DG-DG.3: 16 residues within 4Å: Chain A: G.76, S.77, A.80, F.81, P.105, C.106, L.107, G.108, D.109, K.110, V.111 Ligands: DA-DA-DA-DA-DA-DC.2, DA-DA-DA-DA-DA-DC.2, DA-DA-DA-DA-DA-DC.2, DA-DA-DA-DA-DA-DC.2, DA-DA-DA-DA-DA-DC.2 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.233, D.235 Ligands: DA-DA-DA-DA-DA-DC.1, SO4.8 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.5: 4 residues within 4Å: Chain A: T.143, V.145, V.148 Ligands: DA-DA-DA-DA-DA-DC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.143, A:V.148

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

SO4.6: 4 residues within 4Å: Chain A: L.51, K.228, M.229, T.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.229, A:T.230 SO4.7: 2 residues within 4Å: Chain A: K.359, R.370 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.359, A:R.370 SO4.8: 7 residues within 4Å: Chain A: G.222, G.223, R.226, K.228, D.235 Ligands: DA-DA-DA-DA-DA-DC.1, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.223 Water bridges: A:R.226, A:R.226, A:K.228, A:K.228 Salt bridges: A:R.226, A:K.228 SO4.9: 2 residues within 4Å: Ligands: DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.348

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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