MolNFT v1 · #66294 · protein
The structure and conformation of lys-63 linked tetra-ubiquitin
3HM3: “The structure and conformation of lys-63 linked tetra-ubiquitin”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #66294 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HM3
- Type
- protein
- Length
- 304 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- P62988
- Ligands
- ZN
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ubiquitin | protein | 76 | 20% helix, 34% strand | P62988 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- C–D · 100 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 91 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 81 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 isopeptide (isopeptide).
Compared structures
- 3HM3 · The Structure and conformation of Lys-63 linked tetra-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 3HM3 · PDBe 3HM3 · UniProt P62988
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