MolNFT v1 · #81706 · protein
2.4 ångström crystal structure of superantigen-like protein from staphylococcus aureus.
3V05: “2.4 ångström crystal structure of superantigen-like protein from staphylococcus aureus.”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.81). MolNFT v1 #81706 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3V05
- Type
- protein
- Length
- 764 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superantigen-like protein
- UniProt
- Q2G1S5
- Ligands
- CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superantigen-like protein | protein | 193 | 19% helix, 42% strand | Q2G1S5 |
| B | Superantigen-like protein | protein | 192 | 18% helix, 43% strand | Q2G1S5 |
| C | Superantigen-like protein | protein | 187 | 19% helix, 41% strand | Q2G1S5 |
| D | Superantigen-like protein | protein | 192 | 18% helix, 41% strand | Q2G1S5 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.81 | 0.82 | 76 | empty |
| 2 | 416 | 0.70 | 0.81 | 49 | empty |
| 3 | 384 | 0.65 | 0.79 | 44 | empty |
| 4 | 197 | 0.60 | 0.82 | 25 | empty |
| 5 | 222 | 0.60 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1171 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 951 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 726 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3V05 · 2.4 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus. · 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 Q2G1S5
- Elsewhere: RCSB PDB 3V05 · PDBe 3V05 · UniProt Q2G1S5
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