Research workbench
Crystal structure of the RV144 C1-C2 specific antibody CH55 Fab
Analyse Crystal structure of the RV144 C1-C2 specific antibody CH55 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OED
- Type
- protein
- Length
- 1,275 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH55 Fab heavy chain; CH55 Fab light chain
- Pockets
- 16 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CH55 Fab heavy chain | protein | 214 | 6% helix, 49% strand | — |
| L, B, D | CH55 Fab light chain | protein | 213 | 4% helix, 50% strand | — |
| A, C | CH55 Fab heavy chain | protein | 211 | 4% helix, 46% strand | — |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.64 | 0.84 | 19 | empty |
| 2 | 358 | 0.57 | 0.75 | 40 | empty |
| 3 | 385 | 0.55 | 0.74 | 56 | empty |
| 4 | 173 | 0.55 | 0.80 | 23 | empty |
| 5 | 322 | 0.53 | 0.74 | 40 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1827 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1823 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1775 Ų buried · 13 hydrogen bonds · protein-protein
- H–A · 356 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 353 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6OED · Crystal structure of the RV144 C1-C2 specific antibody CH55 Fab · the same entry in another collection · chain H against H, 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 6OED · PDBe 6OED
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