Research workbench
Anti-streptococcus pneumoniae 23F Fab 023.102 with bound rhamnose- galactose
Analyse Anti-streptococcus pneumoniae 23F Fab 023.102 with bound rhamnose- galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HII
- Type
- protein
- Length
- 823 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 023.102 light chain; Fab 023.102 heavy chain
- Ligands
- GAL, RAM
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 023.102 light chain | protein | 212 | 6% helix, 51% strand | — |
| B, D | Fab 023.102 heavy chain | protein | 203 | 6% helix, 54% strand | — |
| C | Fab 023.102 light chain | protein | 205 | 7% helix, 51% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B, C, D
- RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.54 | 0.74 | 50 | empty |
| 2 | 314 | 0.52 | 0.74 | 39 | empty |
| 3 | 87 | 0.37 | 0.75 | 19 | empty |
| 4 | 66 | 0.35 | 0.77 | 18 | RAM |
| 5 | 50 | 0.30 | 0.76 | 16 | RAM |
Interfaces
3 interfaces between chains.
- A–B · 1897 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1873 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 316 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4HII · Anti-Streptococcus pneumoniae 23F Fab 023.102 with bound rhamnose-galactose · 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
- Elsewhere: RCSB PDB 4HII · PDBe 4HII
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