SMTL ID : 8deu.1

Cryo-electron microscopy structure of Neisseria gonorrhoeae multidrug efflux pump MtrD with CASP peptide complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 x CYS- THR- ASN- GLU- ASP- GLY- LYS- PRO- CYS: CASP peptide(Non-covalent)

CYS-THR-ASN-GLU-ASP-GLY-LYS-PRO-CYS.1: 18 residues within 4Å: Chain B: S.87, F.136, R.174, F.176, G.177, A.178, S.275, T.277, A.288, M.290, Y.325, F.568, V.607, F.610, F.612, F.623, I.625, L.668 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.136, B:F.136, B:F.136, B:F.176, B:F.176, B:F.176, B:A.288, B:Y.325, B:L.668 Hydrogen bonds: B:S.87, B:R.174, B:G.177, B:G.177, B:S.275, B:S.275, B:T.277 Salt bridges: B:R.174

27 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)(Non-functional Binders)

PTY.2: 3 residues within 4Å: Chain A: M.1 Ligands: PTY.3, PTY.25 Ligand excluded by PLIP PTY.3: 3 residues within 4Å: Ligands: PTY.2, PTY.20, PTY.25 Ligand excluded by PLIP PTY.4: 6 residues within 4Å: Chain A: I.17 Chain B: V.879, F.882, W.892, F.1040 Ligands: PTY.5 Ligand excluded by PLIP PTY.5: 7 residues within 4Å: Chain A: W.13, I.17, I.20, A.21 Chain B: W.892 Ligands: PTY.4, PTY.13 Ligand excluded by PLIP PTY.6: 6 residues within 4Å: Chain A: I.27, K.28, L.30, P.31 Ligands: PTY.9, PTY.13 Ligand excluded by PLIP PTY.7: 8 residues within 4Å: Chain A: A.878, V.879, F.882, W.892, S.893, L.899, F.1040 Ligands: PTY.8 Ligand excluded by PLIP PTY.8: 8 residues within 4Å: Chain A: V.879, F.882, L.883, W.892 Chain C: W.13, I.17, I.20 Ligands: PTY.7 Ligand excluded by PLIP PTY.9: 5 residues within 4Å: Chain A: V.32, I.339, F.378, I.388 Ligands: PTY.6 Ligand excluded by PLIP PTY.10: 19 residues within 4Å: Chain A: F.11, V.14, I.15, F.18, I.19, A.22, G.376, A.379, F.380, Y.383, F.478 Chain B: G.438, I.441, G.442, A.445, V.884, A.887, L.888 Ligands: PTY.11 Ligand excluded by PLIP PTY.11: 1 residues within 4Å: Ligands: PTY.10 Ligand excluded by PLIP PTY.12: 5 residues within 4Å: Chain A: M.1, V.452, M.456, A.477, F.481 Ligand excluded by PLIP PTY.13: 4 residues within 4Å: Chain A: I.368, L.375 Ligands: PTY.5, PTY.6 Ligand excluded by PLIP PTY.14: 8 residues within 4Å: Chain B: M.1, F.4, F.5, I.15, F.481 Ligands: PTY.15, PTY.18, PTY.19 Ligand excluded by PLIP PTY.15: 4 residues within 4Å: Ligands: PTY.14, PTY.19, PTY.24, PTY.26 Ligand excluded by PLIP PTY.16: 14 residues within 4Å: Chain B: W.13, I.17, I.20, A.21, I.24, F.25 Chain C: M.456, F.457, A.872, A.875, L.876, V.879, W.892 Ligands: PTY.22 Ligand excluded by PLIP PTY.17: 15 residues within 4Å: Chain B: I.27, K.28, L.30, V.32, N.296, I.335, V.338, I.339, L.342, P.371, L.374, L.375, F.378, I.388, M.393 Ligand excluded by PLIP PTY.18: 12 residues within 4Å: Chain B: A.22, A.379, F.380, Y.383, M.384, A.473, S.474, A.477, F.478, F.481 Ligands: PTY.14, PTY.19 Ligand excluded by PLIP PTY.19: 12 residues within 4Å: Chain B: F.4, R.8, F.11, I.15, F.18 Chain C: V.884, A.887, L.888 Ligands: PTY.14, PTY.15, PTY.18, PTY.24 Ligand excluded by PLIP PTY.20: 14 residues within 4Å: Chain A: G.438, A.887, L.888 Chain C: F.4, R.8, F.11, I.15, F.18, I.19, A.22, A.379, F.478 Ligands: PTY.3, PTY.25 Ligand excluded by PLIP PTY.21: 5 residues within 4Å: Chain C: M.1, I.441 Ligands: PTY.24, PTY.25, PTY.28 Ligand excluded by PLIP PTY.22: 9 residues within 4Å: Chain B: I.17 Chain C: A.878, V.879, F.882, W.892, L.896, L.899, F.1040 Ligands: PTY.16 Ligand excluded by PLIP PTY.23: 7 residues within 4Å: Chain C: I.27, K.28, L.30, V.32, I.343, L.375 Ligands: PTY.27 Ligand excluded by PLIP PTY.24: 8 residues within 4Å: Chain C: I.441, S.449, V.452, V.884 Ligands: PTY.15, PTY.19, PTY.21, PTY.26 Ligand excluded by PLIP PTY.25: 10 residues within 4Å: Chain C: M.1, F.4, F.5, I.15, F.481 Ligands: PTY.2, PTY.3, PTY.20, PTY.21, PTY.28 Ligand excluded by PLIP PTY.26: 2 residues within 4Å: Ligands: PTY.15, PTY.24 Ligand excluded by PLIP PTY.27: 3 residues within 4Å: Chain C: L.342, F.378 Ligands: PTY.23 Ligand excluded by PLIP PTY.28: 9 residues within 4Å: Chain C: F.380, L.470, A.473, S.474, A.477, F.478, F.481 Ligands: PTY.21, PTY.25 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyu, M. et al., Structural Basis of Peptide-Based Antimicrobial Inhibition of a Resistance-Nodulation-Cell Division Multidrug Efflux Pump. Microbiol Spectr (2022)

Release Date

2022-09-14

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

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