Research workbench
Myelin oligodendrocyte glycoprotein-(8-18C5) Fab-complex
Analyse Myelin oligodendrocyte glycoprotein-(8-18C5) Fab-complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PKQ
- Type
- protein
- Length
- 1,109 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (8-18C5) chimeric Fab, light chain; (8-18C5) chimeric Fab, heavy chain; Myelin…
- UniProt
- Q63345
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (8-18C5) chimeric Fab, light chain | protein | 219 | 5% helix, 50% strand | — |
| B | (8-18C5) chimeric Fab, heavy chain | protein | 221 | 10% helix, 52% strand | — |
| E | Myelin oligodendrocyte glycoprotein | protein | 121 | 10% helix, 49% strand | Q63345 |
| F | (8-18C5) chimeric Fab, light chain | protein | 216 | 5% helix, 50% strand | — |
| G | (8-18C5) chimeric Fab, heavy chain | protein | 214 | 10% helix, 52% strand | — |
| J | Myelin oligodendrocyte glycoprotein | protein | 118 | 13% helix, 50% strand | Q63345 |
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 | 1016 | 0.71 | 0.75 | 96 | empty |
| 2 | 665 | 0.70 | 0.78 | 64 | empty |
| 3 | 320 | 0.68 | 0.82 | 47 | empty |
| 4 | 345 | 0.66 | 0.81 | 45 | empty |
| 5 | 178 | 0.47 | 0.75 | 25 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1771 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1690 Ų buried · 15 hydrogen bonds · protein-protein
- G–J · 636 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 612 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 432 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1PKQ · Myelin Oligodendrocyte Glycoprotein-(8-18C5) Fab-complex · the same entry in another collection · chain J against J, TM-score 1.00
- Q63345 · AlphaFold monomer V2.0 prediction for myelin-oligodendrocyte glycoprotein (Q63345) · a predicted model of the same protein · chain J 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 Q63345
- Elsewhere: RCSB PDB 1PKQ · PDBe 1PKQ · UniProt Q63345
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