MolNFT v1 · #137254 · protein
Crystal structure of polyubiquitin with 3 ub domains, domains 1 and 2, from naegleria fowleri atcc 30863
5VIX: “Crystal structure of polyubiquitin with 3 ub domains, domains 1 and 2, from naegleria fowleri atcc 30863”. X-ray diffraction, 1 ligand (NO3), 2 pockets (best druggability 0.38). MolNFT v1 #137254 on GenesisL1: 3D structure, binding…
- PDB
- 5VIX
- Type
- protein
- Length
- 154 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin
- UniProt
- D2V6G7
- Ligands
- NO3
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyubiquitin | protein | 154 | 24% helix, 36% strand | D2V6G7 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.38 | 0.79 | 18 | empty |
| 2 | 58 | 0.29 | 0.75 | 9 | empty |
Compared structures
- 5VIX · Crystal structure of Polyubiquitin with 3 ub domains, domains 1 and 2, from Naegleria… · 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 D2V6G7
- Elsewhere: RCSB PDB 5VIX · PDBe 5VIX · UniProt D2V6G7
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