Research workbench
Anti-streptococcus pneumoniae 23F Fab 023.102 with bound L-rhamnose- (1-2)-alpha-D-galactose-(3-O)-phosphate-2-glycerol
Analyse Anti-streptococcus pneumoniae 23F Fab 023.102 with bound L-rhamnose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HIJ
- Type
- protein
- Length
- 826 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
- MBG, RAM, PO4
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 023.102 light chain | protein | 209 | 7% helix, 51% strand | — |
| B | Fab 023.102 heavy chain | protein | 203 | 6% helix, 54% strand | — |
| C | Fab 023.102 light chain | protein | 212 | 5% helix, 50% strand | — |
| D | Fab 023.102 heavy chain | protein | 202 | 6% helix, 54% strand | — |
Ligands and binding sites
- MBG · methyl beta-D-galactopyranoside · ligand · 2 copies · chains A, C, D
- RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 2 copies · chains B, 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 | 379 | 0.56 | 0.74 | 53 | empty |
| 2 | 276 | 0.50 | 0.74 | 37 | empty |
| 3 | 82 | 0.37 | 0.76 | 22 | empty |
| 4 | 65 | 0.32 | 0.76 | 16 | RAM, PO4 |
| 5 | 56 | 0.29 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1889 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1879 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 328 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4HIJ · Anti-Streptococcus pneumoniae 23F Fab 023.102 with bound… · 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 4HIJ · PDBe 4HIJ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.