MolNFT v1 · #137759 · protein
Structure of single chain fel D 1 bound to a neutralizing antibody
5VYF · Antibody light chain: “Structure of single chain fel D 1 bound to a neutralizing antibody”. X-ray diffraction, 1 ligand (CA), 14 pockets (best druggability 0.76). MolNFT v1 #137759 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VYF
- Type
- protein
- Length
- 1,108 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Antibody Fab heavy chain; Chimera of major allergen I polypeptide…
- UniProt
- P30440, P30438
- Ligands
- CA
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody light chain | protein | 213 | 6% helix, 51% strand | — |
| H | Antibody Fab heavy chain | protein | 206 | 4% helix, 51% strand | — |
| F | Chimera of major allergen I polypeptide chain 2,MAJOR allergen I polypeptide chain 1 | protein | 137 | 78% helix, 0% strand | P30440, P30438 |
| A | Antibody light chain | protein | 211 | 6% helix, 51% strand | — |
| B | Antibody Fab heavy chain | protein | 205 | 4% helix, 52% strand | — |
| C | Chimera of major allergen I polypeptide chain 2,MAJOR allergen I polypeptide chain 1 | protein | 136 | 79% helix, 0% strand | P30440, P30438 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.76 | 0.98 | 17 | CA |
| 2 | 81 | 0.76 | 0.98 | 18 | CA |
| 3 | 204 | 0.55 | 0.79 | 27 | empty |
| 4 | 60 | 0.55 | 0.89 | 19 | empty |
| 5 | 185 | 0.54 | 0.79 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1673 Ų buried · 9 hydrogen bonds · protein-protein
- L–H · 1639 Ų buried · 10 hydrogen bonds · protein-protein
- L–A · 801 Ų buried · 20 hydrogen bonds · protein-protein
- H–F · 607 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 596 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5VYF · Structure of single chain Fel d 1 bound to a neutralizing antibody · the same entry in another collection · chain B against B, TM-score 1.00
- P30438 · AlphaFold monomer V2.0 prediction for major allergen I polypeptide chain 1 (P30438) · a predicted model of the same protein · chain F against A, TM-score 0.50
- P30440 · AlphaFold monomer V2.0 prediction for major allergen I polypeptide chain 2 (P30440) · a predicted model of the same protein · chain F against A, TM-score 0.48
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 P30440
- Every structure of UniProt P30438
- Elsewhere: RCSB PDB 5VYF · PDBe 5VYF · UniProt P30440 · UniProt P30438
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