MolNFT v1 · #69284 · protein
Crystal structure of a vimentin fragment
3KLT: “Crystal structure of a vimentin fragment”. X-ray diffraction, 2 ligands (CA, SM), 2 pockets (best druggability 0.80). MolNFT v1 #69284 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KLT
- Type
- protein
- Length
- 283 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vimentin
- UniProt
- P08670
- Ligands
- CA, SM
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vimentin | protein | 71 | 94% helix, 0% strand | P08670 |
| C | Vimentin | protein | 71 | 93% helix, 0% strand | P08670 |
| D | Vimentin | protein | 70 | 96% helix, 0% strand | P08670 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains B, D
- SM · Samarium (III) ion · metal · 3 copies · chains A, B, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, C, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A, C
- P6G · Hexaethylene glycol · additive · chains B, D
- 1PE · Pentaethylene glycol · additive · chains B, D
- PGE · Triethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.80 | 0.97 | 16 | CA |
| 2 | 1198 | 0.79 | 0.80 | 60 | P33, P6G, PG4, 1PE |
Interfaces
6 interfaces between chains.
- A–B · 1039 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 922 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 792 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 733 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 707 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KLT · Crystal structure of a vimentin 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 3KLT · PDBe 3KLT · UniProt P08670
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