MolNFT v1 · #167452 · protein
Anti-peg antibody 6-3 Fab fragment in complex with peg
6VL9 · 6-3 Fab heavy chain: “Anti-peg antibody 6-3 Fab fragment in complex with peg”. X-ray diffraction, 1 ligand (9FO), 9 pockets (best druggability 0.79). MolNFT v1 #167452 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VL9
- Type
- protein
- Length
- 854 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-3 Fab heavy chain; 6-3 Fab light chain
- Ligands
- 9FO
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 6-3 Fab heavy chain | protein | 210 | 9% helix, 50% strand | — |
| L | 6-3 Fab light chain | protein | 218 | 6% helix, 52% strand | — |
| A | 6-3 Fab heavy chain | protein | 209 | 10% helix, 51% strand | — |
| B | 6-3 Fab light chain | protein | 217 | 6% helix, 51% strand | — |
Ligands and binding sites
- 9FO · 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57-nonadecaoxanonapentacontane-1,59-diol · ligand · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.79 | 0.81 | 89 | empty |
| 2 | 903 | 0.73 | 0.77 | 78 | empty |
| 3 | 89 | 0.54 | 0.85 | 22 | empty |
| 4 | 177 | 0.53 | 0.79 | 35 | empty |
| 5 | 115 | 0.49 | 0.80 | 22 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1589 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1490 Ų buried · 8 hydrogen bonds · protein-protein
- L–B · 445 Ų buried · 6 hydrogen bonds · protein-protein
- L–A · 270 Ų buried · 5 hydrogen bonds · protein-protein
- H–B · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6VL9 · Anti-PEG antibody 6-3 Fab fragment in complex with PEG · the same entry in another collection · chain H against H, 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 6VL9 · PDBe 6VL9
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