Research workbench
Crystal structure of adalimumab Fab fragment
Analyse Crystal structure of adalimumab Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NYL
- Type
- protein
- Length
- 1,449 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adalimumab light chain; Adalimumab heavy chain
- Pockets
- 11 · best druggability 0.58
Structure
x-ray diffraction · 8 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Adalimumab light chain | protein | 211 | 5% helix, 51% strand | — |
| H | Adalimumab heavy chain | protein | 212 | 4% helix, 50% strand | — |
| B | Adalimumab light chain | protein | 117 | 0% helix, 44% strand | — |
| A | Adalimumab heavy chain | protein | 199 | 3% helix, 45% strand | — |
| D | Adalimumab light chain | protein | 211 | 7% helix, 49% strand | — |
| C | Adalimumab heavy chain | protein | 213 | 6% helix, 51% strand | — |
| F | Adalimumab light chain | protein | 124 | 2% helix, 45% strand | — |
| E | Adalimumab heavy chain | protein | 162 | 4% helix, 39% strand | — |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.58 | 0.73 | 59 | empty |
| 2 | 433 | 0.57 | 0.74 | 53 | empty |
| 3 | 469 | 0.57 | 0.73 | 54 | empty |
| 4 | 339 | 0.54 | 0.74 | 39 | empty |
| 5 | 222 | 0.49 | 0.74 | 40 | empty |
Interfaces
8 interfaces between chains.
- L–H · 1713 Ų buried · 12 hydrogen bonds · protein-protein
- D–C · 1667 Ų buried · 7 hydrogen bonds · protein-protein
- F–E · 1072 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 866 Ų buried · 3 hydrogen bonds · protein-protein
- L–D · 353 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 4NYL · Crystal structure of adalimumab FAB fragment · the same entry in another collection · chain L against L, 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 4NYL · PDBe 4NYL
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