Research workbench
Structure of MEDI8852 Fab fragment
Analyse Structure of MEDI8852 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JW5
- Type
- protein
- Length
- 862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MEDI8852 heavy chain; MEDI8852 light chain
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | MEDI8852 heavy chain | protein | 224 | 6% helix, 52% strand | — |
| L | MEDI8852 light chain | protein | 209 | 6% helix, 53% strand | — |
| A | MEDI8852 heavy chain | protein | 223 | 6% helix, 52% strand | — |
| B | MEDI8852 light chain | protein | 206 | 6% helix, 53% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.76 | 0.83 | 55 | empty |
| 2 | 760 | 0.71 | 0.77 | 50 | empty |
| 3 | 68 | 0.46 | 0.83 | 16 | empty |
| 4 | 66 | 0.45 | 0.82 | 19 | empty |
| 5 | 97 | 0.44 | 0.79 | 18 | PO4 |
Interfaces
6 interfaces between chains.
- A–B · 1684 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1683 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 577 Ų buried · 3 hydrogen bonds · protein-protein
- L–B · 313 Ų buried · 6 hydrogen bonds · protein-protein
- H–B · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5JW5 · Structure of MEDI8852 Fab Fragment · the same entry in another collection · chain H against H, 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 5JW5 · PDBe 5JW5
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