MolNFT v1 · #49256 · protein
Crystal structure of ykqa from bacillus subtilis. northeast structural genomics target SR631
2QIK · UPF0131 protein ykqa: “Crystal structure of ykqa from bacillus subtilis. northeast structural genomics target SR631”. X-ray diffraction, 5 pockets (best druggability 0.62). MolNFT v1 #49256 on GenesisL1: 3D structure, binding sites…
- PDB
- 2QIK
- Type
- protein
- Length
- 269 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0131 protein ykqa
- UniProt
- P39759
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0131 protein ykqa | protein | 269 | 26% helix, 41% strand | P39759 |
Ligands and binding sites
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.62 | 0.93 | 15 | empty |
| 2 | 114 | 0.57 | 0.84 | 22 | CIT |
| 3 | 78 | 0.49 | 0.83 | 13 | empty |
| 4 | 111 | 0.45 | 0.78 | 24 | empty |
| 5 | 79 | 0.45 | 0.81 | 24 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2QIK · Crystal structure of YkqA from Bacillus subtilis. Northeast Structural Genomics Target… · the same entry in another collection · chain A against A, TM-score 1.00
- P39759 · AlphaFold monomer V2.0 prediction for putative gamma- glutamylcyclotransferase ykqa… · 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 P39759
- Elsewhere: RCSB PDB 2QIK · PDBe 2QIK · UniProt P39759
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