SMTL ID : 4ea8.1

X-ray crystal structure of PerB from Caulobacter crescentus in complex with coenzyme A and GDP-N-acetylperosamine at 1 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 15 residues within 4Å: Chain A: N.139, H.155, P.158, F.173, G.175, V.176, G.193, A.194, I.209, K.216 Chain C: I.181, P.182, V.199, P.212 Ligands: JB3.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.209 Hydrogen bonds: A:V.176, A:A.194, A:A.194, A:K.216 COA.5: 15 residues within 4Å: Chain A: I.181, P.182, V.199, P.212 Chain B: N.139, H.155, P.158, F.173, G.175, V.176, G.193, A.194, I.209, K.216 Ligands: JB3.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.209 Hydrogen bonds: B:V.176, B:A.194, B:A.194, B:K.216 COA.9: 15 residues within 4Å: Chain B: 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, K.216 Ligands: JB3.10 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.209 Hydrogen bonds: C:V.176, C:A.194, C:A.194, C:K.216

3 x JB3: GDP-N-acetylperosamine(Non-covalent)

JB3.2: 22 residues within 4Å: Chain A: I.18, G.20, 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, P.158 Chain C: D.145, H.146, A.163, G.164, P.182 Ligands: COA.1 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:P.158, C:D.145 Hydrogen bonds: A:G.22, A:H.23, A:V.42, A:A.44, A:D.45, A:G.79, C:H.146, C:G.164 Water bridges: A:G.21, A:A.24, A:D.60, A:D.80, A:N.139 Salt bridges: A:D.43, A:D.60 JB3.6: 22 residues within 4Å: Chain A: D.145, H.146, A.163, G.164, P.182 Chain B: I.18, G.20, 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, P.158 Ligands: COA.5 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.158, A:D.145 Hydrogen bonds: B:G.22, B:H.23, B:V.42, B:A.44, B:D.45, B:G.79, A:H.146, A:G.164 Water bridges: B:G.21, B:A.24, B:D.60, B:D.80, B:N.139 Salt bridges: B:D.43, B:D.60 JB3.10: 22 residues within 4Å: Chain B: D.145, H.146, A.163, G.164, P.182 Chain C: I.18, G.20, 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, P.158 Ligands: COA.9 17 PLIP interactions: 3 interactions with chain B, 14 interactions with chain C Hydrophobic interactions: B:D.145, C:P.158 Hydrogen bonds: B:H.146, B:G.164, 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.80, C:N.139 Salt bridges: C:D.43, C:D.60

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

CL.3: 3 residues within 4Å: Chain A: R.32, T.37, V.38 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: K.214, I.215 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: R.32, T.37, V.38 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: K.214, I.215 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: R.32, T.37, V.38 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: K.214, I.215 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

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