MolNFT v1 · #134956 · protein
Neurospora crassa polysaccharide monooxygenase 2 high mannosylation
5TKF · Lytic polysaccharide monooxygenase: “Neurospora crassa polysaccharide monooxygenase 2 high mannosylation”. X-ray diffraction, 4 ligands (NAG, MAN, CU), 5 pockets (best druggability 0.63). MolNFT v1 #134956 on GenesisL1: 3D…
- PDB
- 5TKF
- Type
- protein
- Length
- 892 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lytic polysaccharide monooxygenase
- UniProt
- Q8WZQ2
- Ligands
- NAG, MAN, CU, OXY
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lytic polysaccharide monooxygenase | protein | 223 | 5% helix, 34% strand | Q8WZQ2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, C
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.63 | 0.74 | 79 | NAG |
| 2 | 142 | 0.51 | 0.80 | 19 | empty |
| 3 | 124 | 0.51 | 0.81 | 18 | OXY |
| 4 | 288 | 0.51 | 0.74 | 38 | empty |
| 5 | 66 | 0.34 | 0.77 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 878 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 436 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 157 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5TKF · Neurospora crassa polysaccharide monooxygenase 2 high mannosylation · 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
- Every structure of UniProt Q8WZQ2
- Elsewhere: RCSB PDB 5TKF · PDBe 5TKF · UniProt Q8WZQ2
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