Research workbench
Crystal structure of mycolic acid transporter MMPL3 from mycobacterium smegmatis complexed with ICA38
Analyse Crystal structure of mycolic acid transporter MMPL3 from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AJJ
- Type
- protein
- Length
- 901 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Drug exporters of the rnd superfamily-like protein, endolysin
- EC
- 3.2.1.17
- UniProt
- I7G2R2, D9IEF7
- Ligands
- L6T, MHA, J9E
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Drug exporters of the rnd superfamily-like protein, endolysin (EC 3.2.1.17) | protein | 901 | 63% helix, 7% strand | I7G2R2, D9IEF7 |
Ligands and binding sites
- L6T · alpha-D-glucopyranosyl 6-O-dodecyl-alpha-D-glucopyranoside · ligand · 5 copies · chains A
- MHA · (carbamoylmethyl-carboxymethyl-amino)-acetic acid · ligand · 2 copies · chains A
- J9E · 4,6-difluoro-N-(spiro[5.5]undecan-3-yl)-1H-indole-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.81 | 0.82 | 86 | L6T |
| 2 | 1065 | 0.78 | 0.80 | 83 | L6T, J9E |
| 3 | 205 | 0.59 | 0.81 | 29 | empty |
| 4 | 176 | 0.48 | 0.76 | 29 | empty |
| 5 | 102 | 0.40 | 0.77 | 23 | MHA |
Compared structures
- 6AJJ · Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis… · the same entry in another collection · chain A against A, TM-score 1.00
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 I7G2R2
- Every structure of UniProt D9IEF7
- Elsewhere: RCSB PDB 6AJJ · PDBe 6AJJ · UniProt I7G2R2 · UniProt D9IEF7
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