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Structure of tandemly arrayed consecutive rib domains (RIB2R) from group B streptococcal species streptococcus agalactiae
Analyse Structure of tandemly arrayed consecutive rib domains (RIB2R) from group B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S5Y
- Type
- protein
- Length
- 1,289 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group B streptococcal R4 surface protein
- UniProt
- P72362
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group B streptococcal R4 surface protein | protein | 163 | 12% helix, 39% strand | P72362 |
| B, C, D, E, F, G | Group B streptococcal R4 surface protein | protein | 161 | 12% helix, 40% strand | P72362 |
| H | Group B streptococcal R4 surface protein | protein | 160 | 12% helix, 39% strand | P72362 |
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.80 | 0.84 | 103 | empty |
| 2 | 1102 | 0.77 | 0.79 | 114 | empty |
| 3 | 1001 | 0.74 | 0.77 | 111 | empty |
| 4 | 229 | 0.68 | 0.85 | 33 | empty |
| 5 | 404 | 0.66 | 0.80 | 51 | empty |
Interfaces
20 interfaces between chains.
- C–E · 773 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 767 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 740 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 735 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 707 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6S5Y · Structure of tandemly arrayed consecutive Rib domains (Rib2R) from Group B Streptococcal… · 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 P72362
- Elsewhere: RCSB PDB 6S5Y · PDBe 6S5Y · UniProt P72362
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