Research workbench
Cryo-EM structure of mycobacterium smegmatis MMPL3 complexed with ST004 in lipid nanodiscs
Analyse Cryo-EM structure of mycobacterium smegmatis MMPL3 complexed with ST004 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WNX
- Type
- protein
- Length
- 734 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trehalose monomycolate exporter MMPL3
- UniProt
- A0QP27
- Ligands
- 1I2
- Pockets
- 8 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trehalose monomycolate exporter MMPL3 | protein | 734 | 63% helix, 5% strand | A0QP27 |
Ligands and binding sites
- 1I2 · N-[2-(2-adamantylamino)ethyl]-1-[2,4-bis(fluoranyl) phenyl]-5-(4-chlorophenyl)-4-methyl-pyrazole-3-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.86 | 0.95 | 42 | 1I2 |
| 2 | 1080 | 0.78 | 0.79 | 78 | empty |
| 3 | 646 | 0.74 | 0.80 | 64 | empty |
| 4 | 92 | 0.38 | 0.76 | 23 | empty |
| 5 | 97 | 0.38 | 0.74 | 16 | empty |
Compared structures
- 7WNX · Cryo-EM structure of Mycobacterium smegmatis MmpL3 complexed with ST004 in lipid nanodiscs · the same entry in another collection · chain A against A, TM-score 1.00
- A0QP27 · AlphaFold monomer V2.0 prediction for trehalose monomycolate exporter MMPL3 (A0QP27) · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0QP27
- Elsewhere: RCSB PDB 7WNX · PDBe 7WNX · UniProt A0QP27
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