SMTL ID : 8j40.1

Crystal Structure of CATB8 in complex with chloramphenicol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-trimer

Ligands

12 x CLM: CHLORAMPHENICOL(Non-covalent)(Covalent)

CLM.1: 13 residues within 4Å: Chain A: P.8, F.9, K.10, G.11, Y.30, S.32 Chain B: Y.46, A.74, Q.77, H.79, Y.91, M.92 Ligands: CLM.13 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.11, A:Y.30, A:S.32, A:S.32, B:H.79 Halogen bonds: A:K.10 Hydrophobic interactions: B:Y.46, B:Q.77 CLM.2: 8 residues within 4Å: Chain A: T.188, A.189, P.191, L.192, G.200, K.203, Y.204, E.207 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.204 Hydrogen bonds: A:E.207 Halogen bonds: A:G.200 CLM.3: 13 residues within 4Å: Chain A: W.118, V.136, G.138, S.139 Chain B: I.72, G.75, N.76, Q.77, H.79, H.81, S.86, M.126, P.127 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.139, B:Q.77 Water bridges: A:S.139, A:S.139 pi-Stacking: A:W.118 Hydrophobic interactions: B:H.79 CLM.4: 8 residues within 4Å: Chain A: L.48, D.50, R.51, Y.91, E.94 Chain C: F.9, K.10 Ligands: CLM.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.51, A:R.51 pi-Stacking: A:Y.91 Halogen bonds: A:D.50 CLM.10: 13 residues within 4Å: Chain B: P.8, F.9, K.10, G.11, Y.30, S.32 Chain C: Y.46, A.74, Q.77, H.79, Y.91, M.92 Ligands: CLM.22 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.46, C:Q.77 Hydrogen bonds: C:H.79, B:G.11, B:S.32, B:S.32 Halogen bonds: B:K.10 CLM.11: 8 residues within 4Å: Chain B: T.188, A.189, P.191, L.192, G.200, K.203, Y.204, E.207 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.204 Hydrogen bonds: B:E.207 Halogen bonds: B:G.200 CLM.12: 13 residues within 4Å: Chain B: W.118, V.136, G.138, S.139 Chain C: I.72, G.75, N.76, Q.77, H.79, H.81, S.86, M.126, P.127 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:H.79 Hydrogen bonds: C:Q.77, B:S.139 Water bridges: B:S.139, B:S.139 pi-Stacking: B:W.118 CLM.13: 8 residues within 4Å: Chain A: F.9, K.10 Chain B: L.48, D.50, R.51, Y.91, E.94 Ligands: CLM.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.51, B:R.51 pi-Stacking: B:Y.91 Halogen bonds: B:D.50 CLM.19: 13 residues within 4Å: Chain A: Y.46, A.74, Q.77, H.79, Y.91, M.92 Chain C: P.8, F.9, K.10, G.11, Y.30, S.32 Ligands: CLM.4 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.11, C:S.32, C:S.32, A:H.79 Halogen bonds: C:K.10 Hydrophobic interactions: A:Y.46, A:Q.77 CLM.20: 8 residues within 4Å: Chain C: T.188, A.189, P.191, L.192, G.200, K.203, Y.204, E.207 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.204 Hydrogen bonds: C:E.207 Halogen bonds: C:G.200 CLM.21: 13 residues within 4Å: Chain A: I.72, G.75, N.76, Q.77, H.79, H.81, S.86, M.126, P.127 Chain C: W.118, V.136, G.138, S.139 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.139, A:Q.77 Water bridges: C:S.139, C:S.139 pi-Stacking: C:W.118 Hydrophobic interactions: A:H.79 CLM.22: 8 residues within 4Å: Chain B: F.9, K.10 Chain C: L.48, D.50, R.51, Y.91, E.94 Ligands: CLM.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.51, C:R.51 pi-Stacking: C:Y.91 Halogen bonds: C:D.50

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: G.11, E.12, L.13 Chain B: M.92, E.94 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.11, A:L.13, B:E.94, B:E.94 GOL.6: 4 residues within 4Å: Chain A: L.13, S.15, R.27, Y.28 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:E.95, A:S.15, A:S.29 Hydrogen bonds: A:S.15, A:Y.28 GOL.7: 6 residues within 4Å: Chain A: L.142, T.144, P.157 Chain C: G.154, G.155, I.161 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:S.139, C:G.155, A:T.144 GOL.8: 6 residues within 4Å: Chain A: Y.4, F.5, N.6, S.7, K.10, G.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.6, A:S.7, A:S.7 Water bridges: A:E.12 GOL.14: 5 residues within 4Å: Chain B: G.11, E.12, L.13 Chain C: M.92, E.94 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.11, B:L.13, C:E.94, C:E.94 GOL.15: 4 residues within 4Å: Chain B: L.13, S.15, R.27, Y.28 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.15, B:Y.28 Water bridges: B:S.15, B:Y.28, B:S.29, C:E.95 GOL.16: 6 residues within 4Å: Chain A: G.154, G.155, I.161 Chain B: L.142, T.144, P.157 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.139, A:G.155 GOL.17: 6 residues within 4Å: Chain B: Y.4, F.5, N.6, S.7, K.10, G.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.6, B:S.7, B:S.7 Water bridges: B:E.12, B:E.12 GOL.23: 5 residues within 4Å: Chain A: M.92, E.94 Chain C: G.11, E.12, L.13 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:E.94, C:G.11, C:L.13 GOL.24: 4 residues within 4Å: Chain C: L.13, S.15, R.27, Y.28 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.15, C:Y.28 Water bridges: C:S.15, C:Y.28, C:S.29 GOL.25: 6 residues within 4Å: Chain B: G.154, G.155, I.161 Chain C: L.142, T.144, P.157 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.139, B:G.155 GOL.26: 6 residues within 4Å: Chain C: Y.4, F.5, N.6, S.7, K.10, G.11 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.6, C:S.7, C:S.7 Water bridges: C:E.12, C:E.12

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 2 residues within 4Å: Chain A: N.115, N.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.115, A:N.180, A:N.180 SO4.18: 2 residues within 4Å: Chain B: N.115, N.180 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.115, B:N.180, B:N.180 Water bridges: B:E.177 SO4.27: 2 residues within 4Å: Chain C: N.115, N.180 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.115, C:N.180, C:N.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liao, J. et al., Chloramphenicol Binding Sites of Acinetobacter baumannii Chloramphenicol Acetyltransferase CatB8. Acs Infect Dis. (2024)

Release Date

2024-02-28

Peptides

CatB8: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

CatB8