Research workbench
Structure of ESX-3 complex
Analyse Structure of ESX-3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LAR
- Type
- protein
- Length
- 3,020 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Mycolicibacterium smegmatis MC2 155
- Molecule
- ESX-3 secretion system ATPase EccB3; ESX-3 secretion system protein EccD3; ESX-3…
- EC
- 3.6.-.-
- UniProt
- A0QQ39, A0QQ46, A0QQ40, A0QQ48
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.7 · 7 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ESX-3 secretion system ATPase EccB3 (EC 3.6.-.-) | protein | 81 | 47% helix, 1% strand | A0QQ39 |
| B, E | ESX-3 secretion system protein EccD3 | protein | 427 | 62% helix, 7% strand | A0QQ46 |
| C, H | ESX-3 secretion system protein EccD3 | protein | 442 | 62% helix, 5% strand | A0QQ46 |
| F | ESX-3 secretion system protein EccC3 | protein | 336 | 28% helix, 14% strand | A0QQ40 |
| G, D | ESX-3 secretion system protein EccE3 | protein | 241 | 35% helix, 20% strand | A0QQ48 |
| I | ESX-3 secretion system ATPase EccB3 (EC 3.6.-.-) | protein | 59 | 75% helix, 0% strand | A0QQ39 |
| J | ESX-3 secretion system protein EccC3 | protein | 324 | 28% helix, 15% strand | A0QQ40 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.82 | 0.83 | 99 | empty |
| 2 | 195 | 0.78 | 0.93 | 32 | empty |
| 3 | 446 | 0.75 | 0.84 | 48 | empty |
| 4 | 58 | 0.72 | 0.98 | 18 | empty |
| 5 | 386 | 0.70 | 0.82 | 58 | empty |
Interfaces
24 interfaces between chains.
- B–C · 3130 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 3020 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1313 Ų buried · 3 hydrogen bonds · protein-protein
- H–I · 1312 Ų buried · 3 hydrogen bonds · protein-protein
- E–D · 1010 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6LAR · Structure of esx-3 complex · the same entry in another collection · chain J against J, TM-score 1.00
- A0QQ40 · AlphaFold monomer V2.0 prediction for esx-3 secretion system protein ECCC3 (A0QQ40) · a predicted model of the same protein · chain J against A, TM-score 0.97
- A0QQ48 · AlphaFold monomer V2.0 prediction for esx-3 secretion system protein ECCE3 (A0QQ48) · a predicted model of the same protein · chain G against A, TM-score 0.95
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 A0QQ39
- Every structure of UniProt A0QQ46
- Every structure of UniProt A0QQ40
- Every structure of UniProt A0QQ48
- Elsewhere: RCSB PDB 6LAR · PDBe 6LAR · UniProt A0QQ39 · UniProt A0QQ46 · UniProt A0QQ40 · UniProt A0QQ48
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