Research workbench
Structure of an intact ESX-5 inner membrane complex, Composite C3 model
Analyse Structure of an intact ESX-5 inner membrane complex, Composite C3 model in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NPR
- Type
- protein
- Length
- 11,992 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.82
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- ESX-5 secretion system ATPase EccB5; ESX-5 secretion system protein EccC5; ESX-5…
- EC
- 3.6.-.-, 3.4.21.-
- UniProt
- P9WNQ9, P9WNA5, P9WNP9, O53945
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.82 · 7 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B1, B2, B3 | ESX-5 secretion system ATPase EccB5 (EC 3.6.-.-) | protein | 478 | 23% helix, 26% strand | P9WNQ9 |
| B4, B5, B6 | ESX-5 secretion system ATPase EccB5 (EC 3.6.-.-) | protein | 480 | 25% helix, 25% strand | P9WNQ9 |
| C1, C2, C3, C4, C5, C6 | ESX-5 secretion system protein EccC5 | protein | 406 | 40% helix, 18% strand | P9WNA5 |
| D1, D3, D5, D7, D9, DB | ESX-5 secretion system protein EccD5 | protein | 485 | 65% helix, 9% strand | P9WNP9 |
| D2, D6, D8, DA, DC | ESX-5 secretion system protein EccD5 | protein | 405 | 68% helix, 8% strand | P9WNP9 |
| D4 | ESX-5 secretion system protein EccD5 | protein | 415 | 67% helix, 8% strand | P9WNP9 |
| P1, P2, P3 | Mycosin-5 (EC 3.4.21.-) | protein | 444 | 27% helix, 16% strand | O53945 |
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 | 1089 | 0.85 | 0.86 | 118 | empty |
| 2 | 1014 | 0.85 | 0.86 | 113 | empty |
| 3 | 907 | 0.85 | 0.86 | 103 | empty |
| 4 | 1049 | 0.80 | 0.81 | 104 | empty |
| 5 | 997 | 0.80 | 0.81 | 110 | empty |
Interfaces
99 interfaces between chains.
- D3–D4 · 3652 Ų buried · 19 hydrogen bonds · protein-protein
- D7–D8 · 3622 Ų buried · 21 hydrogen bonds · protein-protein
- D1–D2 · 3612 Ų buried · 21 hydrogen bonds · protein-protein
- DB–DC · 3603 Ų buried · 18 hydrogen bonds · protein-protein
- D5–D6 · 3587 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- O53945 · AlphaFold monomer V2.0 prediction for mycosin-5 (O53945) · a predicted model of the same protein · chain P1 against A, TM-score 0.86
- P9WNA5 · AlphaFold monomer V2.0 prediction for esx-5 secretion system protein ECCC5 (P9WNA5) · a predicted model of the same protein · chain C3 against A, TM-score 0.86
- P9WNQ9 · AlphaFold monomer V2.0 prediction for esx-5 secretion system ATPase ECCB5 (P9WNQ9) · a predicted model of the same protein · chain B1 against A, TM-score 0.84
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 P9WNQ9
- Every structure of UniProt P9WNA5
- Every structure of UniProt P9WNP9
- Every structure of UniProt O53945
- Elsewhere: RCSB PDB 7NPR · PDBe 7NPR · UniProt P9WNQ9 · UniProt P9WNA5 · UniProt P9WNP9 · UniProt O53945
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