Research workbench
Crystal structure of ACPA E4 in complex with CII-C-48-CIT
Analyse Crystal structure of ACPA E4 in complex with CII-C-48-CIT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OCY
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- ACPA E4 Fab fragment - heavy chain; ACPA E4 Fab fragment - light chain; Cii-C-48-cit
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | ACPA E4 Fab fragment - heavy chain | protein | 211 | 3% helix, 55% strand | — |
| L | ACPA E4 Fab fragment - light chain | protein | 214 | 8% helix, 50% strand | — |
| C | Cii-C-48-cit | protein | 9 | 0% helix, 11% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.67 | 0.76 | 55 | empty |
| 2 | 99 | 0.42 | 0.78 | 23 | empty |
| 3 | 75 | 0.32 | 0.75 | 19 | empty |
| 4 | 60 | 0.28 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1838 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 427 Ų buried · 9 hydrogen bonds · protein-protein
- L–C · 308 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, cyclization, nonstandard).
Compared structures
- 5OCY · Crystal structure of acpa E4 in complex with cii-C-48-cit · 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 5OCY · PDBe 5OCY
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