MolNFT v1 · #137395 · protein
Crystal structure of human yeats domain
5VNA · Yeats domain-containing protein 4: “Crystal structure of human yeats domain”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.75). MolNFT v1 #137395 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VNA
- Type
- protein
- Length
- 508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeats domain-containing protein 4
- UniProt
- O95619
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yeats domain-containing protein 4 | protein | 134 | 6% helix, 51% strand | O95619 |
| B | Yeats domain-containing protein 4 | protein | 125 | 4% helix, 50% strand | O95619 |
| C | Yeats domain-containing protein 4 | protein | 124 | 2% helix, 52% strand | O95619 |
| D | Yeats domain-containing protein 4 | protein | 125 | 7% helix, 58% strand | O95619 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains B, D
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.75 | 0.78 | 87 | EDO, NHE |
| 2 | 224 | 0.45 | 0.73 | 26 | SO4 |
| 3 | 147 | 0.42 | 0.75 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–C · 653 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 349 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 257 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 173 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 O95619
- Elsewhere: RCSB PDB 5VNA · PDBe 5VNA · UniProt O95619
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