MolNFT v1 · #56588 · protein
Crystal structure of secye translocon from thermus thermophilus with a Fab fragment
2ZJS · Preprotein translocase secy subunit: “Crystal structure of secye translocon from thermus thermophilus with a Fab fragment”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.67). MolNFT v1 #56588 on GenesisL1: 3D…
- PDB
- 2ZJS
- Type
- protein
- Length
- 895 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Preprotein translocase secy subunit; Preprotein translocase sece subunit; FAB56 (heavy…
- UniProt
- Q8KZP3, Q8KZP4
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | Preprotein translocase secy subunit | protein | 415 | 70% helix, 5% strand | Q8KZP3 |
| E | Preprotein translocase sece subunit | protein | 46 | 52% helix, 0% strand | Q8KZP4 |
| H | FAB56 (heavy chain) | protein | 220 | 6% helix, 51% strand | — |
| L | FAB56 (light chain) | protein | 214 | 4% helix, 46% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains Y, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.67 | 0.93 | 18 | empty |
| 2 | 400 | 0.66 | 0.79 | 41 | empty |
| 3 | 397 | 0.61 | 0.76 | 28 | empty |
| 4 | 338 | 0.59 | 0.77 | 34 | empty |
| 5 | 177 | 0.54 | 0.79 | 28 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1944 Ų buried · 19 hydrogen bonds · protein-protein
- Y–E · 1752 Ų buried · 4 hydrogen bonds · protein-protein
- Y–L · 404 Ų buried · 5 hydrogen bonds · protein-protein
- Y–H · 373 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2ZJS · Crystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment · the same entry in another collection · chain Y against Y, 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
- Every structure of UniProt Q8KZP3
- Every structure of UniProt Q8KZP4
- Elsewhere: RCSB PDB 2ZJS · PDBe 2ZJS · UniProt Q8KZP3 · UniProt Q8KZP4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.