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Crystal structure of vimentin (fragment 144-251) from homo sapiens, northeast structural genomics consortium target HR4796B
Analyse Crystal structure of vimentin (fragment 144-251) from homo sapiens, northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UF1
- Type
- protein
- Length
- 431 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vimentin
- UniProt
- P08670
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vimentin | protein | 104 | 93% helix, 0% strand | P08670 |
| B | Vimentin | protein | 106 | 91% helix, 0% strand | P08670 |
| C | Vimentin | protein | 109 | 92% helix, 0% strand | P08670 |
| D | Vimentin | protein | 112 | 93% helix, 0% strand | P08670 |
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 | 259 | 0.62 | 0.80 | 28 | empty |
| 2 | 214 | 0.53 | 0.77 | 25 | empty |
| 3 | 55 | 0.38 | 0.79 | 11 | empty |
| 4 | 118 | 0.35 | 0.73 | 16 | empty |
| 5 | 117 | 0.34 | 0.72 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2976 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 2908 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 734 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 726 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 592 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3UF1 · Crystal Structure of Vimentin (fragment 144-251) from Homo sapiens, Northeast Structural… · 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 3UF1 · PDBe 3UF1 · UniProt P08670
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