MolNFT v1 · #170625 · protein
X-ray structure of lpmo
6YDC · Lpmo lytic polysaccharide monooxygenase: “X-ray structure of lpmo”. X-ray diffraction, 3 ligands (BGC, CU, SO4), 4 pockets (best druggability 0.45). MolNFT v1 #170625 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YDC
- Type
- protein
- Length
- 896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lpmo lytic polysaccharide monooxygenase
- UniProt
- A0A223GEC9
- Ligands
- BGC, CU, SO4
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lpmo lytic polysaccharide monooxygenase | protein | 224 | 7% helix, 32% strand | A0A223GEC9 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.45 | 0.74 | 30 | empty |
| 2 | 141 | 0.43 | 0.75 | 20 | empty |
| 3 | 166 | 0.43 | 0.74 | 20 | empty |
| 4 | 121 | 0.41 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 508 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 506 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 188 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, methylation).
Compared structures
- 6YDC · X-ray structure of LPMO · 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 A0A223GEC9
- Elsewhere: RCSB PDB 6YDC · PDBe 6YDC · UniProt A0A223GEC9
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