MolNFT v1 · #123559 · protein
Antibody Fab fragment complex
5JO4 · D80 Fab heavy chain: “Antibody Fab fragment complex”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.59). MolNFT v1 #123559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JO4
- Type
- protein
- Length
- 866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D80 Fab heavy chain; D80 Fab light chain; G6 Fab heavy chain; G6 Fab light chain
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D80 Fab heavy chain | protein | 221 | 10% helix, 50% strand | — |
| B | D80 Fab light chain | protein | 215 | 7% helix, 52% strand | — |
| C | G6 Fab heavy chain | protein | 221 | 5% helix, 48% strand | — |
| D | G6 Fab light chain | protein | 209 | 6% helix, 47% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.59 | 0.80 | 37 | empty |
| 2 | 206 | 0.53 | 0.77 | 29 | empty |
| 3 | 260 | 0.49 | 0.74 | 47 | empty |
| 4 | 243 | 0.47 | 0.73 | 42 | empty |
| 5 | 153 | 0.47 | 0.77 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1784 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1775 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 415 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 108 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5JO4 · Antibody Fab Fragment Complex · the same entry in another collection · chain A against A, 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 5JO4 · PDBe 5JO4
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