MolNFT v1 · #6134 · protein
Catalytic antibody 4B2 in complex with its amidinium hapten.
1F3D: “Catalytic antibody 4B2 in complex with its amidinium hapten.”. X-ray diffraction, 2 ligands (TPM, SO4), 9 pockets (best druggability 0.74). MolNFT v1 #6134 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1F3D
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalytic antibody 4B2
- Ligands
- TPM, SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, J | Catalytic antibody 4B2 | protein | 218 | 6% helix, 51% strand | — |
| H | Catalytic antibody 4B2 | protein | 217 | 7% helix, 51% strand | — |
| K | Catalytic antibody 4B2 | protein | 215 | 8% helix, 51% strand | — |
Ligands and binding sites
- TPM · 2-(4-aminobenzylamino)-3,4,5,6-tetrahydropyridinium · ligand · 2 copies · chains L, H, J, K
- SO4 · Sulfate ion · ion · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.74 | 0.81 | 62 | TPM |
| 2 | 147 | 0.63 | 0.85 | 24 | TPM |
| 3 | 272 | 0.50 | 0.74 | 43 | empty |
| 4 | 274 | 0.50 | 0.74 | 47 | empty |
| 5 | 185 | 0.47 | 0.75 | 30 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1799 Ų buried · 18 hydrogen bonds · protein-protein
- J–K · 1768 Ų buried · 12 hydrogen bonds · protein-protein
- H–J · 537 Ų buried · 7 hydrogen bonds · protein-protein
- L–K · 268 Ų buried · 5 hydrogen bonds · protein-protein
- L–J · 100 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1F3D · Catalytic antibody 4B2 in complex with its amidinium hapten. · 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
- Elsewhere: RCSB PDB 1F3D · PDBe 1F3D
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