Research workbench
Crystal structure of the meningitis pathogen streptococcus suis adhesion fhb
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
- 5BOB
- Type
- protein
- Length
- 996 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 (if-2 GTPase)
- UniProt
- A4VT01
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 (if-2 GTPase) | protein | 203 | 17% helix, 43% strand | A4VT01 |
| B | Translation initiation factor 2 (if-2 GTPase) | protein | 199 | 17% helix, 45% strand | A4VT01 |
| C | Translation initiation factor 2 (if-2 GTPase) | protein | 198 | 18% helix, 44% strand | A4VT01 |
| D | Translation initiation factor 2 (if-2 GTPase) | protein | 200 | 17% helix, 45% strand | A4VT01 |
| E | Translation initiation factor 2 (if-2 GTPase) | protein | 196 | 17% helix, 44% strand | A4VT01 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.82 | 0.83 | 134 | empty |
| 2 | 424 | 0.71 | 0.82 | 49 | empty |
| 3 | 563 | 0.59 | 0.73 | 45 | empty |
| 4 | 201 | 0.55 | 0.80 | 25 | empty |
| 5 | 81 | 0.48 | 0.82 | 23 | empty |
Interfaces
9 interfaces between chains.
- B–E · 617 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 540 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 512 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 382 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 5BOB · Crystal Structure of the Meningitis Pathogen Streptococcus suis adhesion Fhb · 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 A4VT01
- Elsewhere: RCSB PDB 5BOB · PDBe 5BOB · UniProt A4VT01
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