Research workbench
Crystal structure the Fab fragment of efalizumab in complex with lfa-1 I domain, form I
Analyse Crystal structure the Fab fragment of efalizumab in complex with lfa-1 I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EOA
- Type
- protein
- Length
- 1,216 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Efalizumab Fab fragment, light chain; Efalizumab Fab fragment, heavy chain; Integrin…
- UniProt
- P20701
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Efalizumab Fab fragment, light chain | protein | 214 | 5% helix, 50% strand | — |
| H, B | Efalizumab Fab fragment, heavy chain | protein | 215 | 6% helix, 53% strand | — |
| I, J | Integrin alpha-L | protein | 179 | 37% helix, 23% strand | P20701 |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.68 | 0.78 | 43 | empty |
| 2 | 521 | 0.68 | 0.78 | 41 | empty |
| 3 | 689 | 0.65 | 0.74 | 64 | empty |
| 4 | 653 | 0.64 | 0.74 | 66 | empty |
| 5 | 245 | 0.61 | 0.80 | 25 | empty |
Interfaces
9 interfaces between chains.
- L–H · 1855 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1824 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 652 Ų buried · 11 hydrogen bonds · protein-protein
- B–J · 647 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 176 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3EOA · Crystal structure the Fab fragment of Efalizumab in complex with LFA-1 I domain, Form I · the same entry in another collection · chain I against I, TM-score 1.00
- P20701 · AlphaFold monomer V2.0 prediction for integrin alpha-L (P20701) · a predicted model of the same protein · chain I against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P20701
- Elsewhere: RCSB PDB 3EOA · PDBe 3EOA · UniProt P20701
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