Research workbench
Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74
Analyse Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YXK
- Type
- protein
- Length
- 447 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- ACPA 3F3 Fab fragment - heavy chain; ACPA 3F3 Fab fragment - light chain; Citrullinated…
- UniProt
- P08670
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · resolution 2 · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ACPA 3F3 Fab fragment - heavy chain | protein | 220 | 10% helix, 52% strand | — |
| B | ACPA 3F3 Fab fragment - light chain | protein | 218 | 6% helix, 51% strand | — |
| C | Citrullinated Vimentin (59-74) | protein | 9 | 0% helix, 11% strand | P08670 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.62 | 0.75 | 57 | empty |
| 2 | 175 | 0.52 | 0.78 | 30 | empty |
| 3 | 61 | 0.30 | 0.75 | 15 | empty |
| 4 | 56 | 0.26 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1729 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 350 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 335 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
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 P08670
- Elsewhere: RCSB PDB 6YXK · PDBe 6YXK · UniProt P08670
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