MolNFT v1 · #120073 · protein
LYS11-linked diubiquitin
5GOC: “LYS11-linked diubiquitin”. X-ray diffraction, 1 ligand (NA). MolNFT v1 #120073 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GOC
- Type
- protein
- Length
- 146 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; D-ubiquitin
- UniProt
- P0CG47
- Ligands
- NA
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 73 | 21% helix, 36% strand | P0CG47 |
| D | D-ubiquitin | protein | 73 | 25% helix, 34% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–D · 285 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 68 d-amino, 1 modified (D-amino acid, nonstandard).
Compared structures
- 5GOC · Lys11-linked diubiquitin · 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 P0CG47
- Elsewhere: RCSB PDB 5GOC · PDBe 5GOC · UniProt P0CG47
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