Research workbench
Crystal structure of the meningitis pathogen streptococcus suis adhesion fhb bound to the disaccharide receptor GB2
Analyse Crystal structure of the meningitis pathogen streptococcus suis adhesion fhb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BOA
- Type
- protein
- Length
- 1,169 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 (if-2 GTPase)
- UniProt
- A4VT01
- Ligands
- GAL, GLA
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 (if-2 GTPase) | protein | 194 | 20% helix, 43% strand | A4VT01 |
| B | Translation initiation factor 2 (if-2 GTPase) | protein | 198 | 18% helix, 43% strand | A4VT01 |
| C | Translation initiation factor 2 (if-2 GTPase) | protein | 198 | 17% helix, 44% strand | A4VT01 |
| D | Translation initiation factor 2 (if-2 GTPase) | protein | 196 | 17% helix, 44% strand | A4VT01 |
| E | Translation initiation factor 2 (if-2 GTPase) | protein | 191 | 17% helix, 43% strand | A4VT01 |
| F | Translation initiation factor 2 (if-2 GTPase) | protein | 192 | 18% helix, 43% strand | A4VT01 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- GLA · alpha-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.75 | 0.82 | 65 | empty |
| 2 | 662 | 0.74 | 0.81 | 65 | empty |
| 3 | 363 | 0.73 | 0.84 | 47 | empty |
| 4 | 296 | 0.69 | 0.84 | 32 | empty |
| 5 | 317 | 0.57 | 0.77 | 31 | GAL, GLA |
Interfaces
9 interfaces between chains.
- A–D · 522 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 443 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 379 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 301 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 301 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5BOA · Crystal Structure of the Meningitis Pathogen Streptococcus suis adhesion Fhb bound to the… · the same entry in another collection · chain B against B, 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 A4VT01
- Elsewhere: RCSB PDB 5BOA · PDBe 5BOA · UniProt A4VT01
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