MolNFT v1 · #50275 · protein
Crystal structure of staphylococcal superantigen-like protein 11
2RDH: “Crystal structure of staphylococcal superantigen-like protein 11”. X-ray diffraction, 2 ligands (NA, PO4), 6 pockets (best druggability 0.78). MolNFT v1 #50275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2RDH
- Type
- protein
- Length
- 758 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superantigen-like protein 11
- UniProt
- A8E1U5
- Ligands
- NA, PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superantigen-like protein 11 | protein | 185 | 19% helix, 45% strand | A8E1U5 |
| B | Superantigen-like protein 11 | protein | 190 | 19% helix, 43% strand | A8E1U5 |
| C | Superantigen-like protein 11 | protein | 192 | 19% helix, 44% strand | A8E1U5 |
| D | Superantigen-like protein 11 | protein | 191 | 20% helix, 43% strand | A8E1U5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.78 | 0.80 | 109 | PO4 |
| 2 | 881 | 0.75 | 0.79 | 95 | PO4 |
| 3 | 208 | 0.46 | 0.74 | 26 | empty |
| 4 | 96 | 0.43 | 0.79 | 20 | empty |
| 5 | 64 | 0.35 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 891 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 853 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 162 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 108 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2RDH · Crystal structure of Staphylococcal Superantigen-Like protein 11 · the same entry in another collection · chain D against D, TM-score 1.00
- A8E1U5 · AlphaFold monomer V2.0 prediction for superantigen-like protein 11 (A8E1U5) · a predicted model of the same protein · chain A 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 A8E1U5
- Elsewhere: RCSB PDB 2RDH · PDBe 2RDH · UniProt A8E1U5
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