MolNFT v1 · #139882 · protein
Sufs-sufu complex from bacillus subtilis
5XT5 · Zinc-dependent sulfurtransferase sufu: “Sufs-sufu complex from bacillus subtilis”. X-ray diffraction, 2 ligands (PLP, ZN), 11 pockets (best druggability 0.75). MolNFT v1 #139882 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5XT5
- Type
- protein
- Length
- 1,082 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc-dependent sulfurtransferase sufu; Cysteine desulfurase sufs
- EC
- 2.-.-.-, 2.8.1.7
- UniProt
- O32163, O32164
- Ligands
- PLP, ZN
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Zinc-dependent sulfurtransferase sufu (EC 2.-.-.-) | protein | 137 | 45% helix, 18% strand | O32163 |
| A | Cysteine desulfurase sufs (EC 2.8.1.7) | protein | 405 | 44% helix, 18% strand | O32164 |
| B | Cysteine desulfurase sufs (EC 2.8.1.7) | protein | 405 | 44% helix, 18% strand | O32164 |
| C | Zinc-dependent sulfurtransferase sufu (EC 2.-.-.-) | protein | 135 | 50% helix, 20% strand | O32163 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains D, B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.75 | 0.87 | 54 | empty |
| 2 | 82 | 0.74 | 0.97 | 36 | PLP |
| 3 | 74 | 0.72 | 0.97 | 34 | PLP |
| 4 | 556 | 0.68 | 0.78 | 56 | empty |
| 5 | 387 | 0.66 | 0.80 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3566 Ų buried · 56 hydrogen bonds · protein-protein
- D–B · 707 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 11 hydrogen bonds · protein-protein
- D–A · 390 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 218 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5XT5 · SufS-SufU complex from Bacillus subtilis · the same entry in another collection · chain C against C, TM-score 1.00
- O32164 · AlphaFold monomer V2.0 prediction for cysteine desulfurase sufs (O32164) · a predicted model of the same protein · chain B against A, TM-score 1.00
- O32163 · AlphaFold monomer V2.0 prediction for zinc-dependent sulfurtransferase sufu (O32163) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 O32163
- Every structure of UniProt O32164
- Elsewhere: RCSB PDB 5XT5 · PDBe 5XT5 · UniProt O32163 · UniProt O32164
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