MolNFT v1 · #19585 · protein
Lectin uea-II complexed with nag
1QOO · Chitin binding lectin, uea-II: “Lectin uea-II complexed with nag”. X-ray diffraction, 3 ligands (NAG, MN, CA), 5 pockets (best druggability 0.82). MolNFT v1 #19585 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1QOO
- Type
- protein
- Length
- 942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitin binding lectin, uea-II
- Ligands
- NAG, MN, CA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitin binding lectin, uea-II | protein | 234 | 6% helix, 44% strand | — |
| B, C, D | Chitin binding lectin, uea-II | protein | 236 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.82 | 0.84 | 103 | empty |
| 2 | 140 | 0.62 | 0.85 | 23 | empty |
| 3 | 155 | 0.62 | 0.85 | 22 | empty |
| 4 | 132 | 0.60 | 0.84 | 25 | empty |
| 5 | 156 | 0.58 | 0.82 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 889 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 885 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 763 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 759 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 86 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (O-glycosylation, disulfide).
Compared structures
- 1QOO · lectin UEA-II complexed with NAG · 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 1QOO · PDBe 1QOO
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