Research workbench
Crystal structure of Fab of natalizumab in complex with Fab of NAA32.
Analyse Crystal structure of Fab of natalizumab in complex with Fab of NAA32. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FG1
- Type
- protein
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab NAA32; Light chain of Fab NAA32; Heavy chain of Fab natalizumab; Light…
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain of Fab NAA32 | protein | 236 | 9% helix, 49% strand | — |
| D | Light chain of Fab NAA32 | protein | 213 | 4% helix, 50% strand | — |
| H | Heavy chain of Fab natalizumab | protein | 218 | 7% helix, 56% strand | — |
| L | Light chain of Fab natalizumab | protein | 211 | 6% helix, 52% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · 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 | 239 | 0.73 | 0.88 | 35 | empty |
| 2 | 623 | 0.64 | 0.75 | 66 | GOL |
| 3 | 475 | 0.58 | 0.73 | 59 | empty |
| 4 | 208 | 0.53 | 0.77 | 31 | empty |
| 5 | 99 | 0.34 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2079 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1914 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 465 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 291 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 252 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6FG1 · Crystal structure of Fab of natalizumab in complex with Fab of NAA32. · 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 6FG1 · PDBe 6FG1
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