SMTL ID : 3pky.1

Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA, UTP and Manganese.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

1 x DG- DC- DG- DG- DC: DNA 5'-D(P*GP*CP*GP*GP*C)-3'(Non-covalent)

DG-DC-DG-DG-DC.1: 23 residues within 4Å: Chain A: T.15, N.16, K.19, K.29, R.56, P.58, F.66, S.74, Q.107, A.109 Chain B: F.66, F.67, E.68, K.69, Q.70, R.87, S.88, T.91, T.239 Chain C: C.3, G.4, C.5 Ligands: UTP.5 Protein-ligand interaction information (PLIP) not available

2 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.2: 17 residues within 4Å: Chain A: F.67, H.114, D.140, D.142, S.175, S.177, K.178, G.179, H.181, Q.233, T.239, T.240, I.241, R.247 Chain C: A.6 Ligands: MN.3, MN.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:H.114, A:S.175, A:S.175, A:S.177, A:K.178, A:G.179, A:Q.233, A:T.239, A:I.241 Water bridges: A:T.239, A:T.239 Salt bridges: A:H.181, A:R.247 UTP.5: 17 residues within 4Å: Chain B: F.67, H.114, D.140, D.142, S.175, S.177, K.178, G.179, H.181, Q.233, T.239, T.240, I.241, R.247 Ligands: DG-DC-DG-DG-DC.1, MN.6, MN.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.175, B:S.175, B:S.177, B:K.178, B:G.179, B:Q.233, B:T.239, B:T.239, B:I.241 Salt bridges: B:H.181, B:R.247

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 5 residues within 4Å: Chain A: D.140, D.142, H.181 Ligands: UTP.2, MN.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.140, A:D.142 MN.4: 6 residues within 4Å: Chain A: D.140, D.142, D.230, Q.233 Ligands: UTP.2, MN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.140, A:D.142, A:D.230, H2O.1 MN.6: 5 residues within 4Å: Chain B: D.140, D.142, H.181 Ligands: UTP.5, MN.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.140, B:D.142 MN.7: 5 residues within 4Å: Chain B: D.140, D.142, D.230 Ligands: UTP.5, MN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.140, B:D.142, B:D.230, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brissett, N.C. et al., Structure of a Preternary Complex Involving a Prokaryotic NHEJ DNA Polymerase. Mol.Cell (2011)

Release Date

2011-02-16

Peptides

Putative DNA ligase-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative DNA ligase-like protein

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