MolNFT v1 · #148756 · protein
Crystal structure of Fab of natalizumab in complex with Fab of NAA84.
6FG2 · Heavy chain Fab NAA84: “Crystal structure of Fab of natalizumab in complex with Fab of NAA84.”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.81). MolNFT v1 #148756 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6FG2
- Type
- protein
- Length
- 1,724 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain Fab NAA84; Light chain Fab NAA84; Heavy chain Fab natalizumab; Light chain…
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F | Heavy chain Fab NAA84 | protein | 225 | 5% helix, 49% strand | — |
| E, G | Light chain Fab NAA84 | protein | 211 | 9% helix, 46% strand | — |
| H | Heavy chain Fab natalizumab | protein | 212 | 4% helix, 52% strand | — |
| I | Heavy chain Fab natalizumab | protein | 218 | 4% helix, 53% strand | — |
| L, M | Light chain Fab natalizumab | protein | 211 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.81 | 0.83 | 138 | empty |
| 2 | 258 | 0.59 | 0.79 | 38 | empty |
| 3 | 482 | 0.59 | 0.74 | 53 | empty |
| 4 | 332 | 0.56 | 0.75 | 34 | empty |
| 5 | 419 | 0.56 | 0.74 | 53 | empty |
Interfaces
15 interfaces between chains.
- F–G · 1964 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1952 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1950 Ų buried · 12 hydrogen bonds · protein-protein
- I–M · 1948 Ų buried · 15 hydrogen bonds · protein-protein
- D–G · 456 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6FG2 · Crystal structure of Fab of natalizumab in complex with Fab of NAA84. · the same entry in another collection · chain D against D, 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 6FG2 · PDBe 6FG2
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