MolNFT v1 · #120399 · protein
Crystal structure of catalytic domain of protein O-mannosyl kinase in complexes with AMP-pnp, magnesium ions and glycopeptide
5GZ9 · Protein O-mannose kinase: “Crystal structure of catalytic domain of protein O-mannosyl kinase in complexes with AMP-pnp, magnesium ions…”. X-ray diffraction, 3 ligands (ANP, MAN, MG), 2 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 5GZ9
- Type
- protein
- Length
- 280 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-mannose kinase
- EC
- 2.7.1.-
- UniProt
- Q3TUA9
- Ligands
- ANP, MAN, MG
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-mannose kinase (EC 2.7.1.-) | protein | 280 | 38% helix, 20% strand | Q3TUA9 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- MG · Magnesium ion · metal · 2 copies · 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 | 346 | 0.64 | 0.79 | 47 | ANP, MG, MAN |
| 2 | 130 | 0.38 | 0.74 | 28 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5GZ9 · Crystal structure of catalytic domain of Protein O-mannosyl Kinase in complexes with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q3TUA9 · AlphaFold monomer V2.0 prediction for protein O-mannose kinase (Q3TUA9) · a predicted model of the same protein · 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 Q3TUA9
- Elsewhere: RCSB PDB 5GZ9 · PDBe 5GZ9 · UniProt Q3TUA9
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