SMTL ID : 3vbi.1

Crystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 20 residues within 4Å: Chain A: Y.107, I.110, D.111, F.113, F.150, M.166, K.168, V.180, P.181 Chain C: S.101, G.144, A.145, G.162, A.163, V.178, G.179, R.183, I.185, K.186 Ligands: 0FX.9 16 PLIP interactions: 9 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:V.178, A:F.113, A:F.113, A:F.150 Hydrogen bonds: C:A.145, C:A.163, C:A.163, C:G.179, A:K.168, A:K.168 Water bridges: C:R.183 Salt bridges: C:R.183, C:K.186, C:K.186, A:K.168, A:K.168 COA.4: 20 residues within 4Å: Chain A: S.101, G.144, A.145, G.162, A.163, V.178, G.179, R.183, I.185, K.186 Chain B: Y.107, I.110, D.111, F.113, F.150, M.166, K.168, V.180, P.181 Ligands: 0FX.2 21 PLIP interactions: 11 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.178, B:I.110, B:F.113, B:F.113, B:F.150 Hydrogen bonds: A:A.145, A:A.163, A:A.163, A:G.179, A:R.183, B:K.168, B:K.168 Water bridges: A:R.183, A:K.186, A:K.186, B:K.168, B:V.180 Salt bridges: A:K.186, A:K.186, B:K.168, B:K.168 COA.7: 20 residues within 4Å: Chain B: S.101, G.144, A.145, G.162, A.163, V.178, G.179, R.183, I.185, K.186 Chain C: Y.107, I.110, D.111, F.113, F.150, M.166, K.168, V.180, P.181 Ligands: 0FX.5 21 PLIP interactions: 9 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:V.178, C:F.113, C:F.113, C:F.150 Hydrogen bonds: B:A.145, B:A.163, B:A.163, B:G.179, B:R.183, C:K.168 Water bridges: B:K.186, C:K.168, C:K.168, C:K.168, C:K.168, C:K.168, C:K.168 Salt bridges: B:K.186, B:K.186, C:K.168, C:K.168

3 x 0FX: dTDP-4-amino-4,6-dideoxyglucose(Non-covalent)

0FX.2: 18 residues within 4Å: Chain A: M.18, N.19, S.20, F.21, R.60, D.62, D.63, H.78, A.80 Chain B: Y.48, S.68, Y.86, A.109, I.110, D.111, P.121 Ligands: BCT.3, COA.4 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:N.19, A:F.21, B:Y.86 Hydrogen bonds: A:S.20, A:S.20, A:D.63, A:H.78, B:S.68, B:Y.86, B:D.111 Salt bridges: A:R.60, A:R.60 pi-Cation interactions: A:R.60 pi-Stacking: B:Y.48 0FX.5: 17 residues within 4Å: Chain B: M.18, N.19, S.20, R.60, D.62, D.63, H.78, A.80 Chain C: Y.48, S.68, Y.86, A.109, I.110, D.111, P.121 Ligands: BCT.6, COA.7 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:N.19, C:Y.86 Hydrogen bonds: B:S.20, B:S.20, B:R.60, B:D.63, B:H.78, C:S.68, C:D.111 Salt bridges: B:R.60, B:R.60 pi-Cation interactions: B:R.60 Water bridges: C:Y.86, C:Y.86 pi-Stacking: C:Y.48 0FX.9: 17 residues within 4Å: Chain A: Y.48, S.68, Y.86, A.109, I.110, D.111 Chain C: M.18, N.19, S.20, F.21, R.60, D.62, D.63, H.78, A.80 Ligands: COA.1, BCT.10 20 PLIP interactions: 12 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:N.19, C:F.21, A:Y.86 Hydrogen bonds: C:S.20, C:S.20, C:R.60, C:D.62, C:D.63, C:H.78, A:S.68, A:D.111 Water bridges: C:R.60, A:S.68, A:S.68, A:Y.86, A:Y.86 Salt bridges: C:R.60, C:R.60 pi-Cation interactions: C:R.60 pi-Stacking: A:Y.48

3 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.3: 8 residues within 4Å: Chain A: H.78, N.99, I.100, S.101, I.142 Chain B: G.120, P.121 Ligands: 0FX.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.78 BCT.6: 7 residues within 4Å: Chain B: H.78, N.99, I.100, S.101 Chain C: G.120, P.121 Ligands: 0FX.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.100 BCT.10: 7 residues within 4Å: Chain A: D.111, G.120, P.121 Chain C: H.78, N.99, I.100 Ligands: 0FX.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.78

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 6 residues within 4Å: Chain A: Y.82, R.103 Chain B: Y.82, R.103 Chain C: Y.82, R.103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubiak, R.L. et al., Structural Studies of AntD: An N-Acyltransferase Involved in the Biosynthesis of d-Anthrose. Biochemistry (2012)

Release Date

2012-01-25

Peptides

Galactoside O-acetyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

Galactoside O-acetyltransferase

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