MolNFT v1 · #163856 · protein
Atomic resolution structure of splf protease from staphylococcus aureus
6SF7 · Serine protease splf: “Atomic resolution structure of splf protease from staphylococcus aureus”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.67). MolNFT v1 #163856 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SF7
- Type
- protein
- Length
- 789 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease splf
- EC
- 3.4.21.-
- UniProt
- Q2FFT4
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease splf (EC 3.4.21.-) | protein | 202 | 12% helix, 40% strand | Q2FFT4 |
| B | Serine protease splf (EC 3.4.21.-) | protein | 199 | 11% helix, 40% strand | Q2FFT4 |
| C | Serine protease splf (EC 3.4.21.-) | protein | 199 | 10% helix, 41% strand | Q2FFT4 |
| D | Serine protease splf (EC 3.4.21.-) | protein | 189 | 10% helix, 41% strand | Q2FFT4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.67 | 0.82 | 40 | SO4 |
| 2 | 542 | 0.64 | 0.76 | 67 | SO4 |
| 3 | 397 | 0.56 | 0.74 | 59 | SO4 |
| 4 | 67 | 0.56 | 0.88 | 19 | empty |
| 5 | 178 | 0.49 | 0.77 | 28 | SO4 |
Interfaces
5 interfaces between chains.
- C–D · 550 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 371 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SF7 · Atomic resolution structure of SplF protease from Staphylococcus aureus · the same entry in another collection · chain D against D, TM-score 1.00
- Q2FFT4 · AlphaFold monomer V2.0 prediction for serine protease splf (Q2FFT4) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q2FFT4
- Elsewhere: RCSB PDB 6SF7 · PDBe 6SF7 · UniProt Q2FFT4
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