SMTL ID : 6vks.1

Cryo-electron microscopy structures of a gonococcal multidrug efflux pump illuminate a mechanism of drug recognition with ampicillin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

17 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)(Covalent)(Non-functional Binders)

PTY.1: 9 residues within 4Å: Chain A: F.4, R.8, F.11, I.15, F.18 Chain B: G.438, I.441, L.888 Ligands: PTY.4 Ligand excluded by PLIP PTY.2: 5 residues within 4Å: Chain A: W.13, I.17, I.20, T.493 Ligands: PTY.6 Ligand excluded by PLIP PTY.3: 6 residues within 4Å: Chain A: F.882, W.892, F.1040, T.1043 Ligands: PTY.13, PTY.14 Ligand excluded by PLIP PTY.4: 7 residues within 4Å: Chain B: M.1, F.4, F.5, S.437, I.441 Ligands: PTY.1, PTY.5 Ligand excluded by PLIP PTY.5: 6 residues within 4Å: Chain B: F.4, R.8, F.11 Chain C: A.887, L.888 Ligands: PTY.4 Ligand excluded by PLIP PTY.6: 7 residues within 4Å: Chain A: I.17 Chain B: F.882, W.892, L.896, L.899, F.1040 Ligands: PTY.2 Ligand excluded by PLIP PTY.7: 8 residues within 4Å: Chain B: A.21, A.22, I.24, F.25 Chain C: M.456, A.872, A.875 Ligands: PTY.12 Ligand excluded by PLIP PTY.8: 7 residues within 4Å: Chain B: I.27, N.296, I.335, P.371, L.374, L.375, F.378 Ligand excluded by PLIP PTY.10: 13 residues within 4Å: Chain A: G.438, I.441, V.884, L.888, M.1049 Chain C: F.4, R.8, F.11, F.18, I.19, F.478 Ligands: PTY.11, PTY.16 Ligand excluded by PLIP PTY.11: 7 residues within 4Å: Chain A: M.1, I.441 Chain C: K.3, F.4 Ligands: PTY.10, PTY.16, PTY.17 Ligand excluded by PLIP PTY.12: 12 residues within 4Å: Chain B: I.17 Chain C: V.879, F.882, S.891, W.892, S.893, L.896, R.1037, F.1040, K.1041, E.1042 Ligands: PTY.7 Ligand excluded by PLIP PTY.13: 5 residues within 4Å: Chain A: W.892 Chain C: W.13, I.17 Ligands: PTY.3, PTY.14 Ligand excluded by PLIP PTY.14: 5 residues within 4Å: Chain C: W.13, R.361, M.494 Ligands: PTY.3, PTY.13 Ligand excluded by PLIP PTY.15: 4 residues within 4Å: Chain C: I.24, I.27, I.343 Ligands: PTY.18 Ligand excluded by PLIP PTY.16: 9 residues within 4Å: Chain C: M.1, F.4, F.5, F.11, I.15, F.481 Ligands: PTY.10, PTY.11, PTY.17 Ligand excluded by PLIP PTY.17: 2 residues within 4Å: Ligands: PTY.11, PTY.16 Ligand excluded by PLIP PTY.18: 7 residues within 4Å: Chain C: I.27, I.339, L.374, F.378, I.388, M.393 Ligands: PTY.15 Ligand excluded by PLIP

1 x AIX: (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

AIX.9: 5 residues within 4Å: Chain B: F.136, F.176, T.277, V.607, F.610 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.136, B:F.176, B:F.176, B:F.176, B:F.610, B:F.610

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyu, M. et al., Cryo-EM Structures of a Gonococcal Multidrug Efflux Pump Illuminate a Mechanism of Drug Recognition and Resistance. Mbio (2020)

Release Date

2020-07-01

Peptides

Efflux pump membrane transporter: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Efflux pump membrane transporter