Research workbench
Crystal structure of unknown function protein VCA1059
Analyse Crystal structure of unknown function protein VCA1059 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QWV
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0217 protein VC_A1059
- UniProt
- Q9KKP3
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0217 protein VC_A1059 | protein | 188 | 30% helix, 30% strand | Q9KKP3 |
| B | UPF0217 protein VC_A1059 | protein | 197 | 31% helix, 29% strand | Q9KKP3 |
Ligands and binding sites
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.55 | 0.79 | 34 | ACY |
| 2 | 206 | 0.54 | 0.78 | 35 | ACY |
| 3 | 64 | 0.42 | 0.81 | 14 | empty |
| 4 | 57 | 0.30 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1780 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 2QWV · Crystal structure of unknown function protein VCA1059 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KKP3 · AlphaFold monomer V2.0 prediction for putative pseudouridine methyltransferase (Q9KKP3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9KKP3
- Elsewhere: RCSB PDB 2QWV · PDBe 2QWV · UniProt Q9KKP3
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