Research workbench
Crystal structure of basigin complexed with anti-basigin Fab fragment
Analyse Crystal structure of basigin complexed with anti-basigin Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DAA
- Type
- protein
- Length
- 515 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of basigin; Light chain of antibody Fab fragment; Heavy chain of antibody Fab…
- UniProt
- P35613
- Ligands
- CD
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of basigin | protein | 86 | 0% helix, 58% strand | P35613 |
| L | Light chain of antibody Fab fragment | protein | 217 | 7% helix, 52% strand | — |
| H | Heavy chain of antibody Fab fragment | protein | 212 | 7% helix, 52% strand | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 16 copies · chains A, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.63 | 0.75 | 58 | empty |
| 2 | 128 | 0.39 | 0.74 | 25 | CD |
| 3 | 99 | 0.37 | 0.75 | 21 | empty |
| 4 | 65 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1772 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 588 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 419 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, cyclization).
Compared structures
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 7DAA · PDBe 7DAA · UniProt P35613
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