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2.6A crystal structure of psathyrella velutina lectin in complex with N-acetylglucosamine
Analyse 2.6A crystal structure of psathyrella velutina lectin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C4D
- Type
- protein
- Length
- 401 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Psathyrella velutina lectin pvl
- Ligands
- NAG, CA, SO4
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Psathyrella velutina lectin pvl | protein | 401 | 1% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.84 | 0.85 | 86 | empty |
| 2 | 61 | 0.53 | 0.87 | 14 | empty |
Compared structures
- 2C4D · 2.6A Crystal Structure of Psathyrella velutina Lectin in Complex with N-acetylglucosamine · 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 2C4D · PDBe 2C4D
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