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
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acpa 3F3 Fab fragment - heavy chain; Acpa 3F3 Fab fragment - light chain; Citrullinated…
- UniProt
- P08670
- Ligands
- CIR, NAG
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acpa 3F3 Fab fragment - heavy chain | protein | 220 | 10% helix, 51% strand | — |
| B | Acpa 3F3 Fab fragment - light chain | protein | 218 | 6% helix, 51% strand | — |
| C | Citrullinated vimentin (59-74) | protein | 7 | 0% helix, 0% strand | P08670 |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · chains A, B, C
- 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
5 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 | 64 | 0.44 | 0.82 | 21 | CIR |
| 4 | 61 | 0.30 | 0.75 | 15 | empty |
| 5 | 56 | 0.26 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1729 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 205 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 163 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide, 3 glycan (covalent ligand, disulfide, N-glycosylation).
Compared structures
- 6YXK · Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74 · the same entry in another collection · chain A against A, 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
- Every structure of UniProt P08670
- Elsewhere: RCSB PDB 6YXK · PDBe 6YXK · UniProt P08670
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