Research workbench
Structure of a chaperone-substrate complex
Analyse Structure of a chaperone-substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O38
- Type
- protein
- Length
- 4,113 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acinetobacter secreted protease cpaa; Type II secretion chaperone cpab
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 9 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Acinetobacter secreted protease cpaa | protein | 573 | 14% helix, 35% strand | — |
| C | Acinetobacter secreted protease cpaa | protein | 514 | 15% helix, 32% strand | — |
| F | Acinetobacter secreted protease cpaa | protein | 561 | 14% helix, 35% strand | — |
| G | Type II secretion chaperone cpab | protein | 128 | 9% helix, 50% strand | — |
| H | Type II secretion chaperone cpab | protein | 118 | 8% helix, 55% strand | — |
| K | Type II secretion chaperone cpab | protein | 117 | 8% helix, 56% strand | — |
| L | Type II secretion chaperone cpab | protein | 130 | 7% helix, 49% strand | — |
| M | Type II secretion chaperone cpab | protein | 129 | 7% helix, 50% strand | — |
| N | Type II secretion chaperone cpab | protein | 124 | 6% helix, 52% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, G, B, H, C, K, D, L, E, M, F, N
- SO4 · Sulfate ion · ion · 22 copies · chains A, G, B, H, C, K, D, E, F, N, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1054 | 0.87 | 0.88 | 102 | empty |
| 2 | 1089 | 0.87 | 0.88 | 108 | empty |
| 3 | 1100 | 0.86 | 0.87 | 126 | empty |
| 4 | 795 | 0.85 | 0.88 | 77 | empty |
| 5 | 1111 | 0.85 | 0.86 | 108 | empty |
Interfaces
18 interfaces between chains.
- F–N · 2365 Ų buried · 38 hydrogen bonds · protein-protein
- D–L · 2357 Ų buried · 39 hydrogen bonds · protein-protein
- A–G · 2320 Ų buried · 34 hydrogen bonds · protein-protein
- E–M · 2305 Ų buried · 41 hydrogen bonds · protein-protein
- B–H · 2303 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified, 6 disulfide (engineered, disulfide).
Compared structures
- 6O38 · Structure of a chaperone-substrate complex · 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
- Elsewhere: RCSB PDB 6O38 · PDBe 6O38
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