MolNFT v1 · #116095 · protein
Crystal structure of staphylococcal superantigen-like protein 3
5D3D: “Crystal structure of staphylococcal superantigen-like protein 3”. X-ray diffraction, 3 ligands (NA, CL, SCN), 4 pockets (best druggability 0.50). MolNFT v1 #116095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5D3D
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Staphylococcal superantigen-like protein 3
- UniProt
- Q2G0X7
- Ligands
- NA, CL, SCN
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylococcal superantigen-like protein 3 | protein | 190 | 18% helix, 41% strand | Q2G0X7 |
| B | Staphylococcal superantigen-like protein 3 | protein | 195 | 18% helix, 39% strand | Q2G0X7 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
- SCN · Thiocyanate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.50 | 0.78 | 22 | empty |
| 2 | 117 | 0.46 | 0.78 | 26 | GOL, SCN |
| 3 | 67 | 0.38 | 0.79 | 17 | GOL |
| 4 | 73 | 0.34 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5D3D · Crystal structure of Staphylococcal Superantigen-Like protein 3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q2G0X7 · AlphaFold monomer V2.0 prediction for staphylococcal superantigen- like 3 (Q2G0X7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q2G0X7
- Elsewhere: RCSB PDB 5D3D · PDBe 5D3D · UniProt Q2G0X7
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