MolNFT v1 · #114248 · protein
Catalytic domain of coprinopsis cinerea GH62 alpha-L- arabinofuranosidase complexed with pb
5B6T · Glycosyl hydrolase family 62 protein: “Catalytic domain of coprinopsis cinerea GH62 alpha-L- arabinofuranosidase complexed with pb”. X-ray diffraction, 2 ligands (CA, PB), 3 pockets (best druggability 0.63). MolNFT v1 #114248 on…
- PDB
- 5B6T
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 62 protein
- EC
- 3.2.1.55
- UniProt
- A8NI40
- Ligands
- CA, PB
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycosyl hydrolase family 62 protein (EC 3.2.1.55) | protein | 317 | 9% helix, 44% strand | A8NI40 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- PB · Lead (II) ion · metal · chains A
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.63 | 0.77 | 51 | GOL |
| 2 | 102 | 0.45 | 0.79 | 25 | GOL |
| 3 | 96 | 0.43 | 0.79 | 22 | PB, GOL |
Interfaces
1 interface between chains.
- A–B · 273 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5B6T · Catalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuranosidase complexed with Pb · 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 A8NI40
- Elsewhere: RCSB PDB 5B6T · PDBe 5B6T · UniProt A8NI40
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