MolNFT v1 · #41160 · protein
Crystal structure of LYS63-linked di-ubiquitin
2JF5: “Crystal structure of LYS63-linked di-ubiquitin”. X-ray diffraction, 4 ligands (CD, CO, MG). MolNFT v1 #41160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2JF5
- Type
- protein
- Length
- 151 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- P62988
- Ligands
- CD, CO, MG, CL
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 75 | 24% helix, 33% strand | P62988 |
| B | Ubiquitin | protein | 76 | 24% helix, 33% strand | P62988 |
Ligands and binding sites
- CD · Cadmium ion · metal · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 103 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2JF5 · crystal structure of Lys63-linked di-ubiquitin · 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 P62988
- Elsewhere: RCSB PDB 2JF5 · PDBe 2JF5 · UniProt P62988
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