SMTL ID : 3vbj.1

Crystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP and 3-hydroxybutyryl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 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 TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.2: 10 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 16 PLIP interactions: 11 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:D.63, A:D.63, B:S.68 Water bridges: A:R.60, A:R.60, A:R.60, B:S.68, B:S.68 Salt bridges: A:R.60, A:R.60 pi-Cation interactions: A:R.60 pi-Stacking: B:Y.48 TYD.4: 10 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 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:Y.86, B:N.19, B:F.21 Hydrogen bonds: C:S.68, B:S.20, B:D.63, B:D.63 Water bridges: C:G.88, B:R.60, B:R.60 pi-Stacking: C:Y.48 Salt bridges: B:R.60, B:R.60 TYD.6: 10 residues within 4Å: Chain A: Y.48, S.68, Y.86 Chain C: M.18, N.19, S.20, F.21, R.60, D.62, D.63 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:N.19, C:F.21, A:Y.86 Hydrogen bonds: C:S.20, C:D.63, C:D.63, A:S.68 Salt bridges: C:R.60, C:R.60 pi-Stacking: A:Y.48

3 x 3HC: 3-HYDROXYBUTANOYL-COENZYME A(Non-covalent)

3HC.3: 23 residues within 4Å: Chain A: H.78, N.99, I.100, S.101, G.144, A.145, G.162, A.163, V.178, G.179, I.185, K.186 Chain B: Y.107, D.111, F.113, M.119, G.120, P.121, F.150, M.166, K.168, V.180, P.181 21 PLIP interactions: 13 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:N.99, A:V.178, B:F.113, B:F.113, B:F.150 Hydrogen bonds: A:H.78, A:A.145, A:A.163, A:A.163, A:G.179, A:R.183, B:D.111, B:D.111, B:K.168 Water bridges: A:R.183, A:K.186, A:K.186 Salt bridges: A:K.186, A:K.186, B:K.168, B:K.168 3HC.5: 24 residues within 4Å: Chain B: H.78, N.99, I.100, 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, G.120, P.121, F.150, M.166, K.168, V.180, P.181 22 PLIP interactions: 8 interactions with chain C, 14 interactions with chain B Hydrophobic interactions: C:F.113, C:F.113, C:F.150, B:N.99, B:V.178 Hydrogen bonds: C:K.168, C:K.168, B:H.78, B:A.145, B:A.163, B:A.163, B:G.179, B:R.183 Water bridges: C:K.168, B:S.102, B:G.162, B:K.186, B:K.186 Salt bridges: C:K.168, C:K.168, B:K.186, B:K.186 3HC.7: 24 residues within 4Å: Chain A: Y.107, I.110, D.111, F.113, G.120, P.121, F.150, M.166, K.168, V.180, P.181 Chain C: H.78, N.99, I.100, S.101, G.144, A.145, G.162, A.163, V.178, G.179, R.183, I.185, K.186 20 PLIP interactions: 11 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:N.99, 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:D.111, A:K.168, A:K.168 Water bridges: C:R.183, C:R.183, A:K.168 Salt bridges: C:K.186, C:K.186, A:K.168, A:K.168

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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