Research workbench
The structure of the variable domain of streptococcus intermedius antigen I/II (pas)
Analyse The structure of the variable domain of streptococcus intermedius antigen I/II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E36
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable cell-surface antigen I/II
- UniProt
- Q9KW51
- Ligands
- MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable cell-surface antigen I/II | protein | 395 | 20% helix, 32% strand | Q9KW51 |
| B | Probable cell-surface antigen I/II | protein | 393 | 20% helix, 32% strand | Q9KW51 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.72 | 0.77 | 65 | empty |
| 2 | 384 | 0.64 | 0.79 | 41 | empty |
| 3 | 417 | 0.61 | 0.77 | 42 | empty |
| 4 | 75 | 0.35 | 0.76 | 15 | empty |
| 5 | 58 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 161 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6E36 · The structure of the variable domain of Streptococcus intermedius antigen I/II (Pas) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KW51 · AlphaFold monomer V2.0 prediction for probable cell-surface antigen I/II (Q9KW51) · 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 Q9KW51
- Elsewhere: RCSB PDB 6E36 · PDBe 6E36 · UniProt Q9KW51
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