MolNFT v1 · #139883 · protein
A sulfur-transferring catalytic intermediate of sufs-sufu complex from bacillus subtilis
5XT6 · Zinc-dependent sulfurtransferase sufu: “A sulfur-transferring catalytic intermediate of sufs-sufu complex from bacillus subtilis”. X-ray diffraction, 2 ligands (PDA, ZN), 12 pockets (best druggability 0.77). MolNFT v1 #139883 on…
- PDB
- 5XT6
- 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
- PDA, ZN
- Pockets
- 12 · best druggability 0.77
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, 19% 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, 17% strand | O32164 |
| C | Zinc-dependent sulfurtransferase sufu (EC 2.-.-.-) | protein | 135 | 50% helix, 20% strand | O32163 |
Ligands and binding sites
- PDA · 2-[(3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl)-amino]-propionic acid · 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.77 | 0.97 | 32 | PDA |
| 2 | 120 | 0.77 | 0.97 | 34 | PDA |
| 3 | 332 | 0.73 | 0.85 | 42 | empty |
| 4 | 474 | 0.71 | 0.81 | 57 | empty |
| 5 | 460 | 0.70 | 0.80 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3669 Ų buried · 66 hydrogen bonds · protein-protein
- D–B · 683 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 639 Ų buried · 18 hydrogen bonds · protein-protein
- D–A · 373 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 267 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 5XT6 · A sulfur-transferring catalytic intermediate of 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 0.94
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 5XT6 · PDBe 5XT6 · UniProt O32163 · UniProt O32164
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