MolNFT v1 · #104469 · protein
Crystal structure of mycobacterium smegmatis eis in complex with paromomycin
4QB9 · Enhanced intracellular survival protein: “Crystal structure of mycobacterium smegmatis eis in complex with paromomycin”. X-ray diffraction, 2 ligands (PAR, SO4), 20 pockets (best druggability 0.87). MolNFT v1 #104469 on GenesisL1…
- PDB
- 4QB9
- Type
- protein
- Length
- 2,412 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enhanced intracellular survival protein
- UniProt
- A0QY29
- Ligands
- PAR, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Enhanced intracellular survival protein | protein | 402 | 29% helix, 31% strand | A0QY29 |
Ligands and binding sites
- PAR · Paromomycin · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.87 | 0.88 | 109 | empty |
| 2 | 1013 | 0.87 | 0.88 | 108 | empty |
| 3 | 1054 | 0.87 | 0.88 | 107 | empty |
| 4 | 1087 | 0.83 | 0.84 | 110 | PAR, SO4 |
| 5 | 1068 | 0.83 | 0.84 | 108 | PAR, SO4 |
Interfaces
12 interfaces between chains.
- C–D · 1660 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1643 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1633 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 959 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 949 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4QB9 · Crystal structure of Mycobacterium smegmatis Eis in complex with paromomycin · 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 A0QY29
- Elsewhere: RCSB PDB 4QB9 · PDBe 4QB9 · UniProt A0QY29
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