SMTL ID : 3vbl.1

Crystal Structure of the S84C mutant of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 17 residues within 4Å: Chain A: C.101, G.144, A.145, G.162, A.163, V.178, G.179, I.185, K.186 Chain B: Y.107, F.113, F.150, M.166, K.168, V.180, P.181 Ligands: BCT.4 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:V.178, 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 Salt bridges: A:K.186, A:K.186, B:K.168, B:K.168 COA.5: 18 residues within 4Å: Chain B: C.101, G.144, A.145, G.162, A.163, V.178, G.179, R.183, I.185, K.186 Chain C: Y.107, F.113, F.150, M.166, K.168, V.180, P.181 Ligands: BCT.7 16 PLIP interactions: 9 interactions with chain B, 7 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, C:K.168 Water bridges: B:G.162 Salt bridges: B:K.186, B:K.186, C:K.168, C:K.168 COA.8: 18 residues within 4Å: Chain A: Y.107, F.113, F.150, M.166, K.168, V.180, P.181 Chain C: C.101, G.144, A.145, G.162, A.163, V.178, G.179, R.183, I.185, K.186 Ligands: BCT.10 19 PLIP interactions: 11 interactions with chain C, 8 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, C:R.183, A:K.168, A:K.168 Water bridges: C:R.183, C:K.186, C:K.186, A:V.180 Salt bridges: C:K.186, C:K.186, A:K.168, A:K.168

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

CL.2: 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

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

0FX.3: 12 residues within 4Å: Chain A: M.18, N.19, S.20, F.21, R.60, D.62, D.63 Chain B: Y.48, S.68, Y.86, G.88, E.89 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:N.19, A:F.21, B:Y.86 Hydrogen bonds: A:S.20, A:D.63, A:D.63, B:S.68 Salt bridges: A:R.60, A:R.60 pi-Stacking: B:Y.48 0FX.6: 12 residues within 4Å: Chain B: M.18, N.19, S.20, F.21, R.60, D.62, D.63 Chain C: Y.48, S.68, Y.86, G.88, E.89 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:N.19, B:F.21, C:Y.86 Hydrogen bonds: B:S.20, B:D.63, B:D.63, C:S.68 Salt bridges: B:R.60, B:R.60 pi-Stacking: C:Y.48 0FX.9: 12 residues within 4Å: Chain A: Y.48, S.68, Y.86, G.88, E.89 Chain C: M.18, N.19, S.20, F.21, R.60, D.62, D.63 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:Y.86, C:N.19, C:F.21 Hydrogen bonds: A:S.68, C:S.20, C:D.63, C:D.63 Water bridges: A:S.68, A:S.68 pi-Stacking: A:Y.48 Salt bridges: C:R.60, C:R.60

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

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

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