MolNFT v1 · #114278 · protein
Apo structure of cysteine desulfurase from thermococcus onnurineus NA1
5B7S: “Apo structure of cysteine desulfurase from thermococcus onnurineus NA1”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #114278 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B7S
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase
- EC
- 2.8.1.7
- UniProt
- B6YT87
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase (EC 2.8.1.7) | protein | 397 | 42% helix, 16% strand | B6YT87 |
| B | Cysteine desulfurase (EC 2.8.1.7) | protein | 400 | 42% helix, 16% strand | B6YT87 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.69 | 0.83 | 36 | empty |
| 2 | 285 | 0.67 | 0.83 | 36 | empty |
| 3 | 300 | 0.60 | 0.78 | 26 | empty |
| 4 | 156 | 0.47 | 0.77 | 25 | empty |
| 5 | 139 | 0.47 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3610 Ų buried · 69 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 5B7S · Apo structure of Cysteine Desulfurase from Thermococcus onnurineus NA1 · 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
- Every structure of UniProt B6YT87
- Elsewhere: RCSB PDB 5B7S · PDBe 5B7S · UniProt B6YT87
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