MolNFT v1 · #128711 · protein
Formylglycine generating enzyme from T. curvata in complex with CD(II)
5NYY · Non-specific SERINE/THREONINE protein kinase: “Formylglycine generating enzyme from T. curvata in complex with CD(II)”. X-ray diffraction, 2 ligands (CA, CD), 2 pockets (best druggability 0.58). MolNFT v1 #128711 on GenesisL1: 3D…
- PDB
- 5NYY
- Type
- protein
- Length
- 281 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-specific SERINE/THREONINE protein kinase
- EC
- 2.7.11.1
- UniProt
- D1A7C3
- Ligands
- CA, CD
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-specific SERINE/THREONINE protein kinase (EC 2.7.11.1) | protein | 281 | 18% helix, 23% strand | D1A7C3 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- CD · Cadmium ion · metal · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.58 | 0.78 | 26 | CD, MRD, ACT |
| 2 | 52 | 0.32 | 0.78 | 17 | empty |
Compared structures
- 5NYY · Formylglycine generating enzyme from T. curvata in complex with Cd(II) · the same entry in another collection · chain A against A, TM-score 1.00
- D1A7C3 · AlphaFold monomer V2.0 prediction for formylglycine-generating enzyme (D1A7C3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 D1A7C3
- Elsewhere: RCSB PDB 5NYY · PDBe 5NYY · UniProt D1A7C3
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