Research workbench
Crystal structure of CD147 C2 domain in complex with Fab of its monoclonal antibody 6H8
Analyse Crystal structure of CD147 C2 domain in complex with Fab of its monoclonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X0T
- Type
- protein
- Length
- 1,012 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6H8 Fab fragment heavy chain; 6H8 Fab fragment light chain; Basigin
- UniProt
- P35613
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 6H8 Fab fragment heavy chain | protein | 215 | 10% helix, 51% strand | — |
| B, D | 6H8 Fab fragment light chain | protein | 213 | 7% helix, 53% strand | — |
| E, F | Basigin | protein | 78 | 0% helix, 63% strand | P35613 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.73 | 0.83 | 50 | empty |
| 2 | 391 | 0.71 | 0.82 | 42 | empty |
| 3 | 765 | 0.66 | 0.75 | 70 | empty |
| 4 | 459 | 0.63 | 0.77 | 58 | empty |
| 5 | 388 | 0.60 | 0.76 | 55 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1861 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1834 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 448 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 444 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 311 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5X0T · Crystal structure of CD147 C2 domain in complex with Fab of its monoclonal antibody 6H8 · the same entry in another collection · chain F against F, TM-score 1.00
- P35613 · AlphaFold monomer V2.0 prediction for basigin (P35613) · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P35613
- Elsewhere: RCSB PDB 5X0T · PDBe 5X0T · UniProt P35613
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