MolNFT v1 · #114399 · protein
Crystal structure of the meningitis pathogen streptococcus suis adhesion fhb bound to the disaccharide receptor GB2
5BOA · Translation initiation factor 2 (if-2 GTPase): “Crystal structure of the meningitis pathogen streptococcus suis adhesion fhb bound to the disaccharide…”. X-ray diffraction, 2 ligands (GAL, GLA), 11 pockets (best druggability 0.75).…
- 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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