MolNFT v1 · #72981 · protein
Crystal structure of myxococcus xanthus glutaminyl cyclase
3NOK: “Crystal structure of myxococcus xanthus glutaminyl cyclase”. X-ray diffraction, 2 ligands (DDQ, CA), 4 pockets (best druggability 0.75). MolNFT v1 #72981 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NOK
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaminyl cyclase
- EC
- 2.3.2.5
- Ligands
- DDQ, CA
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaminyl cyclase (EC 2.3.2.5) | protein | 234 | 3% helix, 54% strand | — |
| B | Glutaminyl cyclase (EC 2.3.2.5) | protein | 232 | 3% helix, 54% strand | — |
Ligands and binding sites
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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 | 353 | 0.75 | 0.85 | 46 | DDQ |
| 2 | 96 | 0.52 | 0.83 | 23 | empty |
| 3 | 69 | 0.36 | 0.77 | 18 | MES |
| 4 | 61 | 0.33 | 0.77 | 18 | MES |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3NOK · Crystal structure of Myxococcus xanthus Glutaminyl Cyclase · 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
- Elsewhere: RCSB PDB 3NOK · PDBe 3NOK
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