Research workbench
Trimeric crystal structure of vimentin COIL1B fragment
Analyse Trimeric crystal structure of vimentin COIL1B fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YV3
- Type
- protein
- Length
- 215 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vimentin
- UniProt
- P08670
- Ligands
- SO4, CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 95% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vimentin | protein | 77 | 97% helix, 0% strand | P08670 |
| B | Vimentin | protein | 75 | 96% helix, 0% strand | P08670 |
| C | Vimentin | protein | 63 | 92% helix, 0% strand | P08670 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.63 | 0.91 | 21 | empty |
| 2 | 68 | 0.57 | 0.88 | 21 | CL |
| 3 | 60 | 0.27 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1414 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1231 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1115 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4YV3 · Trimeric crystal structure of vimentin coil1B fragment · 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 4YV3 · PDBe 4YV3 · UniProt P08670
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