SMTL ID : 8dew.1

Cryo-electron microscopy structure of Neisseria gonorrhoeae multidrug efflux pump MtrD with LL-37 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

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

PTY.1: 22 residues within 4Å: Chain A: G.438, A.439, I.441, G.442, V.884, A.887, L.888, E.955, H.1053 Chain C: R.8, F.11, V.14, I.15, F.18, I.19, A.22, G.376, A.379, F.380, F.478 Ligands: PTY.3, PTY.21 Ligand excluded by PLIP PTY.2: 15 residues within 4Å: Chain A: M.1, F.4, F.5, R.8, F.11, I.15, I.19, A.477, F.478, F.481 Ligands: PTY.3, PTY.9, PTY.10, PTY.13, PTY.21 Ligand excluded by PLIP PTY.3: 5 residues within 4Å: Chain A: S.437, I.441 Ligands: PTY.1, PTY.2, PTY.21 Ligand excluded by PLIP PTY.4: 8 residues within 4Å: Chain A: W.13, I.17, I.20, A.21, M.494 Chain B: W.892 Ligands: PTY.5, PTY.12 Ligand excluded by PLIP PTY.5: 17 residues within 4Å: Chain A: W.13, I.20, I.24, I.27, K.28, S.29, L.30, P.31, V.32, I.339, I.343, I.368, P.371, I.372, L.375 Ligands: PTY.4, PTY.8 Ligand excluded by PLIP PTY.6: 10 residues within 4Å: Chain A: A.875, A.878, V.879, F.882, W.892, S.893, L.896, L.899, F.1040 Ligands: PTY.7 Ligand excluded by PLIP PTY.7: 11 residues within 4Å: Chain A: V.879, F.882, L.883, W.892, T.1043, H.1045 Chain C: W.13, I.17, I.20, T.493 Ligands: PTY.6 Ligand excluded by PLIP PTY.8: 10 residues within 4Å: Chain A: I.27, V.32, I.339, L.342, M.346, P.371, L.375, F.378, I.388 Ligands: PTY.5 Ligand excluded by PLIP PTY.9: 18 residues within 4Å: Chain A: F.4, F.11, V.14, I.15, F.18, I.19, A.22, A.379, F.380, F.478 Chain B: G.438, I.441, G.442, V.884, A.887, L.888, E.955 Ligands: PTY.2 Ligand excluded by PLIP PTY.10: 10 residues within 4Å: Chain B: M.1, F.4, F.5, F.11, I.15, F.481 Ligands: PTY.2, PTY.11, PTY.13, PTY.16 Ligand excluded by PLIP PTY.11: 9 residues within 4Å: Chain B: F.4, R.8, F.11 Chain C: V.884, A.887, L.888 Ligands: PTY.10, PTY.13, PTY.20 Ligand excluded by PLIP PTY.12: 11 residues within 4Å: Chain A: I.17 Chain B: V.879, F.882, L.883, S.891, W.892, S.893, L.896, L.899, F.1040 Ligands: PTY.4 Ligand excluded by PLIP PTY.13: 5 residues within 4Å: Ligands: PTY.2, PTY.10, PTY.11, PTY.20, PTY.22 Ligand excluded by PLIP PTY.14: 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.18 Ligand excluded by PLIP PTY.15: 16 residues within 4Å: Chain B: I.27, K.28, L.30, V.32, N.296, M.298, 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.16: 14 residues within 4Å: Chain B: I.19, A.22, A.379, F.380, Y.383, M.384, V.452, L.470, A.473, S.474, A.477, F.478, F.481 Ligands: PTY.10 Ligand excluded by PLIP PTY.17: 11 residues within 4Å: Chain C: M.1, I.441, T.444, I.448, A.477, A.480, F.481, L.484 Ligands: PTY.20, PTY.21, PTY.22 Ligand excluded by PLIP PTY.18: 11 residues within 4Å: Chain B: I.17 Chain C: A.878, V.879, F.882, L.883, W.892, S.893, L.896, L.899, F.1040 Ligands: PTY.14 Ligand excluded by PLIP PTY.19: 12 residues within 4Å: Chain C: I.20, I.24, I.27, K.28, L.30, V.32, I.339, I.343, M.346, P.371, L.375 Ligands: PTY.23 Ligand excluded by PLIP PTY.20: 13 residues within 4Å: Chain B: F.18 Chain C: I.441, T.444, A.445, I.448, S.449, V.452, A.880, V.884 Ligands: PTY.11, PTY.13, PTY.17, PTY.22 Ligand excluded by PLIP PTY.21: 14 residues within 4Å: Chain C: M.1, F.4, F.5, F.11, I.15, I.19, F.380, A.477, F.478, F.481 Ligands: PTY.1, PTY.2, PTY.3, PTY.17 Ligand excluded by PLIP PTY.22: 3 residues within 4Å: Ligands: PTY.13, PTY.17, PTY.20 Ligand excluded by PLIP PTY.23: 8 residues within 4Å: Chain C: I.27, I.339, L.342, P.371, L.375, F.378, I.388 Ligands: PTY.19 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
Antibacterial peptide LL-37: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

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

Antibacterial peptide LL-37

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