SMTL ID : 3bac.1

Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: G.164, I.165 Chain B: W.247 Ligands: 3B9.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.165, A:I.165 Water bridges: A:R.180 Salt bridges: A:H.177 PO4.2: 7 residues within 4Å: Chain A: K.53, G.56, A.58, E.111, R.138 Ligands: PO4.3, 3B9.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.58, A:E.111 Salt bridges: A:K.53, A:R.138 PO4.3: 6 residues within 4Å: Chain A: L.19, N.21, K.53 Chain B: A.250, K.252 Ligands: PO4.2 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Salt bridges: B:K.252, A:K.53 Hydrogen bonds: A:L.19, A:N.21, A:N.21, A:N.21 PO4.5: 4 residues within 4Å: Chain A: W.247 Chain B: G.164, I.165 Ligands: 3B9.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.165, B:I.165 Water bridges: B:H.177, B:H.177 Salt bridges: B:H.177 PO4.6: 7 residues within 4Å: Chain B: K.53, G.56, A.58, E.111, R.138 Ligands: PO4.7, 3B9.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.58, B:E.111 Salt bridges: B:K.53, B:R.138 PO4.7: 6 residues within 4Å: Chain A: A.250, K.252 Chain B: L.19, N.21, K.53 Ligands: PO4.6 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.19, B:N.21, B:N.21, B:N.21 Salt bridges: B:K.53, A:K.252

2 x 3B9: N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide(Non-covalent)

3B9.4: 20 residues within 4Å: Chain A: I.14, P.15, M.16, L.17, S.18, L.19, E.51, P.52, K.53, R.109, E.111, Y.163, V.226, K.228, F.240 Chain B: S.242, P.245, W.247 Ligands: PO4.1, PO4.2 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.15, A:L.17, A:L.19, A:F.240, B:W.247, B:W.247 Hydrogen bonds: A:L.17, A:P.52, A:K.53, A:R.109, A:K.228 Salt bridges: A:E.51 pi-Stacking: A:Y.163, A:Y.163, A:F.240 3B9.8: 20 residues within 4Å: Chain A: S.242, P.245, W.247 Chain B: I.14, P.15, M.16, L.17, S.18, L.19, E.51, P.52, K.53, R.109, E.111, Y.163, V.226, K.228, F.240 Ligands: PO4.5, PO4.6 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.15, B:L.17, B:L.19, B:F.240, A:W.247, A:W.247 Hydrogen bonds: B:L.17, B:P.52, B:K.53, B:R.109, B:E.111, B:K.228 Salt bridges: B:E.51 pi-Stacking: B:Y.163, B:Y.163, B:F.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinko, C. et al., Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase. To be Published

Release Date

2008-11-11

Peptides

DNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA ligase