Research workbench
Heptameric espb rosetta model guided by EM density
Analyse Heptameric espb rosetta model guided by EM density in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J83
- Type
- protein
- Length
- 1,932 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esx-1 secretion-associated protein espb
- UniProt
- P9WJD9
- Pockets
- 9 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Esx-1 secretion-associated protein espb | protein | 276 | 66% helix, 0% strand | P9WJD9 |
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.77 | 0.80 | 114 | empty |
| 2 | 955 | 0.76 | 0.79 | 110 | empty |
| 3 | 887 | 0.76 | 0.79 | 104 | empty |
| 4 | 864 | 0.75 | 0.79 | 86 | empty |
| 5 | 866 | 0.74 | 0.79 | 93 | empty |
Interfaces
7 interfaces between chains.
- A–B · 399 Ų buried · 3 hydrogen bonds · protein-protein
- F–G · 397 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 397 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 397 Ų buried · 3 hydrogen bonds · protein-protein
- A–G · 396 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3J83 · Heptameric EspB Rosetta model guided by EM density · the same entry in another collection · chain F against F, TM-score 1.00
- P9WJD9 · AlphaFold monomer V2.0 prediction for esx-1 secretion-associated protein espb (P9WJD9) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P9WJD9
- Elsewhere: RCSB PDB 3J83 · PDBe 3J83 · UniProt P9WJD9
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