Research workbench
Crystal structure of the recombinant Fab fragment derived from the hybridoma M3/38 in complex with a human galectin-3 peptide
Analyse Crystal structure of the recombinant Fab fragment derived from the hybridoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZVF
- Type
- protein
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric Fab M3/38 (L,H); Galectin-3
- UniProt
- P17931
- Ligands
- ACE
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Chimeric Fab M3/38 (L,H) | protein | 219 | 6% helix, 51% strand | — |
| H | Chimeric Fab M3/38 (L,H) | protein | 221 | 10% helix, 51% strand | — |
| P | Galectin-3 | protein | 9 | 33% helix, 0% strand | P17931 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains H, P
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 | 554 | 0.62 | 0.75 | 59 | empty |
| 2 | 54 | 0.52 | 0.88 | 21 | empty |
| 3 | 168 | 0.48 | 0.77 | 28 | empty |
| 4 | 100 | 0.39 | 0.76 | 23 | empty |
| 5 | 63 | 0.31 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1996 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 385 Ų buried · 9 hydrogen bonds · protein-protein
- L–P · 253 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6ZVF · Crystal structure of the recombinant Fab fragment derived from the hybridoma M3/38 in… · the same entry in another collection · chain L against L, 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
- Every structure of UniProt P17931
- Elsewhere: RCSB PDB 6ZVF · PDBe 6ZVF · UniProt P17931
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