SMTL ID : 3mla.2 (1 other biounit)

BaNadD in complex with inhibitor 1_02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

2 x JJZ: 4-[2-(anthracen-9-ylmethylidene)hydrazino]-N-(3-chlorophenyl)-4-oxobutanamide(Non-covalent)

JJZ.1: 19 residues within 4Å: Chain A: I.9, G.10, I.23, T.87, F.105, I.106, I.107, G.108, M.111, Y.114, K.117, W.118, V.133 Chain B: M.111, Y.114, K.117, W.118 Ligands: FMT.5, FMT.8 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.9, A:I.9, A:I.23, A:Y.114, A:W.118, B:Y.114, B:Y.114 Hydrogen bonds: A:G.10, A:G.10, A:G.108 Water bridges: A:N.41 pi-Stacking: A:W.118, B:W.118 JJZ.9: 19 residues within 4Å: Chain C: I.9, G.10, I.23, T.87, F.105, I.106, I.107, G.108, M.111, Y.114, K.117, W.118, V.133 Chain D: M.111, Y.114, K.117, W.118 Ligands: FMT.13, FMT.16 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.9, C:I.9, C:I.23, C:Y.114, C:W.118, D:Y.114, D:Y.114 Hydrogen bonds: C:G.10, C:G.10, C:G.108 Water bridges: C:N.41 pi-Stacking: C:W.118, D:W.118

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 2 residues within 4Å: Chain A: P.84, Y.86 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.86, A:Y.86, A:D.89 FMT.3: 3 residues within 4Å: Chain A: Y.86 Chain B: Y.119, N.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.120, B:N.120 FMT.5: 5 residues within 4Å: Chain A: Y.86, T.87, W.118 Chain B: K.117 Ligands: JJZ.1 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.117, A:T.87, A:T.87 FMT.6: 3 residues within 4Å: Chain B: W.37, S.73, I.74 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.74, B:Y.98 FMT.8: 5 residues within 4Å: Chain A: K.117 Chain B: Y.86, T.87, W.118 Ligands: JJZ.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.87 Water bridges: B:Y.119, A:K.117 FMT.10: 2 residues within 4Å: Chain C: P.84, Y.86 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Y.86, C:Y.86, C:D.89 FMT.11: 3 residues within 4Å: Chain C: Y.86 Chain D: Y.119, N.120 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.120, D:N.120 FMT.13: 5 residues within 4Å: Chain C: Y.86, T.87, W.118 Chain D: K.117 Ligands: JJZ.9 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.117, C:T.87, C:T.87 FMT.14: 3 residues within 4Å: Chain D: W.37, S.73, I.74 2 PLIP interactions: 2 interactions with chain D Water bridges: D:I.74, D:Y.98 FMT.16: 5 residues within 4Å: Chain C: K.117 Chain D: Y.86, T.87, W.118 Ligands: JJZ.9 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.87 Water bridges: D:Y.119, C:K.117

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: W.37, S.73, I.74, C.75, Y.98 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.37, A:W.37 DMS.7: 3 residues within 4Å: Chain B: P.84, S.85, Y.86 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.86, A:N.120 pi-Cation interactions: B:Y.86 DMS.12: 5 residues within 4Å: Chain C: W.37, S.73, I.74, C.75, Y.98 2 PLIP interactions: 2 interactions with chain C pi-Cation interactions: C:W.37, C:W.37 DMS.15: 3 residues within 4Å: Chain D: P.84, S.85, Y.86 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:Y.86, C:N.120 pi-Cation interactions: D:Y.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, N. et al., Complexes of bacterial nicotinate mononucleotide adenylyltransferase with inhibitors: implication for structure-based drug design and improvement. J.Med.Chem. (2010)

Release Date

2010-07-28

Peptides

nicotinate-nucleotide adenylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

nicotinate-nucleotide adenylyltransferase

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