SMTL ID : 6pua.1

The 2.0 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 7 residues within 4Å: Chain A: W.186, E.189, S.190, S.193, L.202, W.206, K.209 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.186 Hydrogen bonds: A:K.209, A:K.209 MPD.7: 7 residues within 4Å: Chain A: W.119, I.137, A.139, S.140 Chain B: G.77, Q.79, M.127 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.119, A:W.119, A:I.137 Hydrogen bonds: A:S.140, A:S.140, A:S.140 Water bridges: B:Q.79 MPD.14: 5 residues within 4Å: Chain B: W.119, A.139, S.140 Chain C: G.77, Q.79 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.119 Hydrogen bonds: B:S.140, B:S.140 Water bridges: B:T.122, B:S.140 MPD.16: 8 residues within 4Å: Chain B: W.186, E.189, S.190, S.193, L.202, N.205, W.206, K.209 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.186, B:W.186 Hydrogen bonds: B:E.189, B:N.205 MPD.20: 8 residues within 4Å: Chain A: G.77, M.127 Chain C: W.119, G.121, I.137, I.138, A.139, S.140 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.119, C:I.137 Hydrogen bonds: C:S.140, C:S.140, C:S.140 Water bridges: C:T.122

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: H.40, D.44 Chain C: Y.36, Y.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.44 EDO.3: 3 residues within 4Å: Chain A: H.116, H.134, N.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.116, A:N.181 Water bridges: A:H.134 EDO.4: 5 residues within 4Å: Chain A: N.5, Y.36, Y.37 Chain B: H.40, D.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.44 EDO.5: 3 residues within 4Å: Chain A: Q.79 Chain C: F.11, S.34 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.11, C:S.34 Water bridges: C:Y.32, C:Y.32 EDO.6: 3 residues within 4Å: Chain A: F.11 Chain B: Q.79 Ligands: PO4.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.32, B:Q.79 EDO.10: 2 residues within 4Å: Chain B: R.82, W.85 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.82, B:R.82 Water bridges: B:D.84, A:S.197, A:S.197 EDO.11: 2 residues within 4Å: Chain B: H.116, N.181 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.181, B:N.181 EDO.12: 2 residues within 4Å: Chain B: F.11 Chain C: Q.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.79 EDO.19: 4 residues within 4Å: Chain B: N.5, Y.36 Chain C: H.40, D.44 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.44 EDO.21: 5 residues within 4Å: Chain B: S.196, S.197 Chain C: R.82, W.85, R.103 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.82, C:R.103, B:S.197 Water bridges: C:R.82

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

CL.8: 3 residues within 4Å: Chain A: N.157 Chain B: N.157 Chain C: N.157 Ligand excluded by PLIP

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 6 residues within 4Å: Chain A: H.50, A.76, Q.79, Y.93, F.106 Chain C: F.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.93 Salt bridges: A:H.50 PO4.13: 4 residues within 4Å: Chain B: F.11 Chain C: H.50, A.76, Y.93 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.50 PO4.15: 5 residues within 4Å: Chain A: F.11 Chain B: H.50, Q.79, Y.93 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.93 Salt bridges: B:H.50 PO4.17: 2 residues within 4Å: Chain C: H.116, N.181 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.134, C:N.181 Salt bridges: C:H.116 PO4.18: 3 residues within 4Å: Chain C: W.186, S.190, W.206 No protein-ligand interaction detected (PLIP) PO4.22: 6 residues within 4Å: Chain A: E.123, R.141 Chain B: E.123, R.141 Chain C: E.123, R.141 7 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 3 interactions with chain C Salt bridges: A:R.141, B:R.141, C:R.141 Water bridges: B:R.141, B:R.141, C:E.123, C:R.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alcala, A. et al., Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species. Protein Sci. (2020)

Release Date

2019-09-25

Peptides

Chloramphenicol acetyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Chloramphenicol acetyltransferase

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