MolNFT v1 · #61429 · protein
Structure of the complex of aquifex aeolicus secyeg and bacillus subtilis seca
3DL8 · Protein translocase subunit seca: “Structure of the complex of aquifex aeolicus secyeg and bacillus subtilis seca”. X-ray diffraction, 20 pockets (best druggability 0.70). MolNFT v1 #61429 on GenesisL1: 3D structure, binding sites…
- 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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