Research workbench
The crystal structure of sclerotium rolfsii lectin in complex with N- acetyl-D-galactosamine
Analyse The crystal structure of sclerotium rolfsii lectin in complex with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OFD
- Type
- protein
- Length
- 282 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sclerotium rolfsii lectin
- Ligands
- ACE, NGA
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sclerotium rolfsii lectin | protein | 141 | 11% helix, 53% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, B
- ACT · Acetate ion · additive · 3 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.38 | 0.74 | 28 | empty |
| 2 | 64 | 0.29 | 0.74 | 16 | empty |
| 3 | 51 | 0.27 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 943 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2OFD · The Crystal Structure of Sclerotium rolfsii lectin in complex with… · 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 2OFD · PDBe 2OFD
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