SMTL ID : 4eab.1

X-ray crystal structure of the H141A mutant of GDP-perosamine N-acetyl transferase from Caulobacter crescentus in complex with CoA and GDP-perosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-trimer

Ligands

3 x JB2: GDP-perosamine(Non-covalent)

JB2.1: 16 residues within 4Å: Chain A: I.18, G.21, G.22, H.23, V.42, D.43, A.44, D.45, D.60, I.78, G.79, L.83, L.87, H.155 Chain B: P.182 Ligands: COA.2 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.22, A:H.23, A:V.42, A:A.44, A:D.45, A:G.79 Water bridges: A:G.21, A:A.24, A:D.60, A:D.60, A:D.80, A:D.80, A:N.139, B:G.164, B:G.164 Salt bridges: A:D.43, A:D.60 JB2.5: 16 residues within 4Å: Chain B: I.18, G.21, G.22, H.23, V.42, D.43, A.44, D.45, D.60, I.78, G.79, L.83, L.87, H.155 Chain C: P.182 Ligands: COA.6 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.22, B:H.23, B:V.42, B:A.44, B:D.45, B:G.79 Water bridges: B:G.21, B:A.24, B:D.60, B:D.60, B:D.80, B:D.80, B:N.139, B:H.155, C:G.164, C:G.164 Salt bridges: B:D.43, B:D.60 JB2.9: 16 residues within 4Å: Chain A: P.182 Chain C: I.18, G.21, G.22, H.23, V.42, D.43, A.44, D.45, D.60, I.78, G.79, L.83, L.87, H.155 Ligands: COA.10 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.22, C:H.23, C:V.42, C:A.44, C:D.45, C:G.79 Water bridges: C:G.21, C:A.24, C:D.60, C:D.60, C:D.80, C:D.80, C:N.139, C:H.155, A:D.145, A:G.164, A:G.164 Salt bridges: C:D.43, C:D.60

3 x COA: COENZYME A(Non-covalent)

COA.2: 14 residues within 4Å: Chain A: N.139, H.155, P.158, F.173, G.175, V.176, G.193, A.194, I.209 Chain B: I.181, P.182, V.199, P.212 Ligands: JB2.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.209 Hydrogen bonds: A:V.176, A:A.194, A:A.194 COA.6: 14 residues within 4Å: Chain B: N.139, H.155, P.158, F.173, G.175, V.176, G.193, A.194, I.209 Chain C: I.181, P.182, V.199, P.212 Ligands: JB2.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.209 Hydrogen bonds: B:V.176, B:A.194, B:A.194 COA.10: 14 residues within 4Å: Chain A: I.181, P.182, V.199, P.212 Chain C: N.139, H.155, P.158, F.173, G.175, V.176, G.193, A.194, I.209 Ligands: JB2.9 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.209 Hydrogen bonds: C:V.176, C:A.194, C:A.194

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Ligands: NA.7, NA.11 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Water bridges: B:G.123, C:G.123, A:G.123 NA.7: 2 residues within 4Å: Ligands: NA.3, NA.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.123, A:G.123 NA.11: 2 residues within 4Å: Ligands: NA.3, NA.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:G.123, C:G.123

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

CL.4: 3 residues within 4Å: Chain A: R.32, T.37, V.38 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.32, T.37, V.38 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: R.32, T.37, V.38 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-ray Crystallographic Studies and Kinetic Analyses. Biochemistry (2012)

Release Date

2012-04-04

Peptides

Perosamine N-acetyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Perosamine N-acetyltransferase