Research workbench
Structure of protomer 2 of the ESX-3 core complex
Analyse Structure of protomer 2 of the ESX-3 core complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SGZ
- Type
- protein
- Length
- 1,505 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.9
- Source
- Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
- Molecule
- ESX-3 secretion system protein EccD3; ESX-3 secretion system ATPase EccB3; ESX-3…
- EC
- 3.6.-.-
- UniProt
- A0QQ46, A0QQ39, A0QQ48
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · resolution 3.9 · 5 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | ESX-3 secretion system protein EccD3 | protein | 435 | 62% helix, 7% strand | A0QQ46 |
| H | ESX-3 secretion system protein EccD3 | protein | 442 | 64% helix, 6% strand | A0QQ46 |
| I | ESX-3 secretion system ATPase EccB3 (EC 3.6.-.-) | protein | 59 | 80% helix, 0% strand | A0QQ39 |
| J | ESX-3 secretion system protein EccC3 | protein | 328 | 30% helix, 16% strand | — |
| D | ESX-3 secretion system protein EccE3 | protein | 241 | 35% helix, 18% strand | A0QQ48 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.75 | 0.93 | 31 | empty |
| 2 | 425 | 0.66 | 0.78 | 41 | empty |
| 3 | 637 | 0.65 | 0.75 | 55 | empty |
| 4 | 55 | 0.61 | 0.92 | 22 | empty |
| 5 | 223 | 0.60 | 0.80 | 24 | empty |
Interfaces
8 interfaces between chains.
- E–H · 3337 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 1367 Ų buried · 7 hydrogen bonds · protein-protein
- E–D · 1104 Ų buried · 2 hydrogen bonds · protein-protein
- H–J · 938 Ų buried · 4 hydrogen bonds · protein-protein
- E–J · 935 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6SGZ · Structure of protomer 2 of the esx-3 core complex · the same entry in another collection · chain J against J, TM-score 1.00
- A0QQ48 · AlphaFold monomer V2.0 prediction for esx-3 secretion system protein ECCE3 (A0QQ48) · a predicted model of the same protein · chain D against A, TM-score 0.95
- A0QQ46 · AlphaFold monomer V2.0 prediction for esx-3 secretion system protein ECCD3 (A0QQ46) · a predicted model of the same protein · chain H against A, TM-score 0.79
- A0QQ39 · AlphaFold monomer V2.0 prediction for esx-3 secretion system ATPase ECCB3 (A0QQ39) · a predicted model of the same protein · chain I against A, TM-score 0.57
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 A0QQ46
- Every structure of UniProt A0QQ39
- Every structure of UniProt A0QQ48
- Elsewhere: RCSB PDB 6SGZ · PDBe 6SGZ · UniProt A0QQ46 · UniProt A0QQ39 · UniProt A0QQ48
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