Research workbench
Structure of the complex of aquifex aeolicus secyeg and bacillus subtilis seca
Analyse Structure of the complex of aquifex aeolicus secyeg and bacillus subtilis seca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DL8
- Type
- protein
- Length
- 2,558 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit seca; Preprotein translocase subunit secy; Sece…
- UniProt
- P28366, O66491, O66505
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein translocase subunit seca | protein | 773 | 51% helix, 8% strand | P28366 |
| G, H | Preprotein translocase subunit secy | protein | 406 | 55% helix, 1% strand | O66491 |
| C, D | Sece | protein | 35 | 94% helix, 0% strand | — |
| E, F | Protein-export membrane protein secg | protein | 65 | 63% helix, 0% strand | O66505 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.70 | 0.75 | 113 | empty |
| 2 | 1156 | 0.69 | 0.75 | 138 | empty |
| 3 | 1014 | 0.69 | 0.74 | 104 | empty |
| 4 | 965 | 0.68 | 0.75 | 95 | empty |
| 5 | 847 | 0.68 | 0.76 | 110 | empty |
Interfaces
10 interfaces between chains.
- A–G · 536 Ų buried · 2 hydrogen bonds · protein-protein
- B–H · 494 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 212 Ų buried · 2 hydrogen bonds · protein-protein
- H–F · 145 Ų buried · 0 hydrogen bonds · protein-protein
- G–E · 136 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3DL8 · Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA · the same entry in another collection · chain F against F, TM-score 1.00
- O66491 · AlphaFold monomer V2.0 prediction for protein translocase subunit secy (O66491) · a predicted model of the same protein · chain G against A, TM-score 0.80
- P28366 · AlphaFold monomer V2.0 prediction for protein translocase subunit seca (P28366) · a predicted model of the same protein · chain A against A, TM-score 0.77
- O66505 · AlphaFold monomer V2.0 prediction for protein-export membrane protein secg (O66505) · a predicted model of the same protein · chain E against A, TM-score 0.63
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 P28366
- Every structure of UniProt O66491
- Every structure of UniProt O66505
- Elsewhere: RCSB PDB 3DL8 · PDBe 3DL8 · UniProt P28366 · UniProt O66491 · UniProt O66505
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