Research workbench
Crystal structure of Fab of natalizumab in complex with Fab of NAA84.
Analyse Crystal structure of Fab of natalizumab in complex with Fab of NAA84. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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