MolNFT v1 · #74105 · protein
Crystal structure of SSU72 with vanadate complex
3OMX · CG14216: “Crystal structure of SSU72 with vanadate complex”. X-ray diffraction, 1 ligand (VO4), 10 pockets (best druggability 0.77). MolNFT v1 #74105 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OMX
- Type
- protein
- Length
- 760 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG14216
- UniProt
- Q9VWE4
- Ligands
- VO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | CG14216 | protein | 190 | 46% helix, 18% strand | Q9VWE4 |
Ligands and binding sites
- VO4 · Vanadate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.77 | 0.81 | 86 | VO4 |
| 2 | 161 | 0.64 | 0.86 | 24 | empty |
| 3 | 268 | 0.60 | 0.79 | 29 | empty |
| 4 | 124 | 0.45 | 0.78 | 29 | VO4 |
| 5 | 75 | 0.44 | 0.81 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 610 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 397 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 375 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 348 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3OMX · Crystal structure of Ssu72 with vanadate complex · 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 Q9VWE4
- Elsewhere: RCSB PDB 3OMX · PDBe 3OMX · UniProt Q9VWE4
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