MolNFT v1 · #172122 · protein
Crystal structure of the fungal lectin CML1
6ZRW · Mucin-binding lectin 1: “Crystal structure of the fungal lectin CML1”. X-ray diffraction, 3 ligands (P3C, PC4, K), 16 pockets (best druggability 0.48). MolNFT v1 #172122 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZRW
- Type
- protein
- Length
- 756 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mucin-binding lectin 1
- UniProt
- B3VS76
- Ligands
- P3C, PC4, K
- Pockets
- 16 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Mucin-binding lectin 1 | protein | 126 | 7% helix, 44% strand | B3VS76 |
Ligands and binding sites
- P3C · Trichloroplatinate · ligand · 4 copies · chains A, C, D, E, F
- PC4 · Tetrachloroplatinate(ii) · ligand · 4 copies · chains A, B, D, F
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 13 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.48 | 0.74 | 28 | GOL, ACT |
| 2 | 70 | 0.35 | 0.76 | 16 | ACT, GOL |
| 3 | 80 | 0.33 | 0.75 | 15 | empty |
| 4 | 78 | 0.33 | 0.75 | 18 | empty |
| 5 | 70 | 0.32 | 0.75 | 16 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1604 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1599 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1595 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 581 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 576 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6ZRW · Crystal structure of the fungal lectin CML1 · 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 B3VS76
- Elsewhere: RCSB PDB 6ZRW · PDBe 6ZRW · UniProt B3VS76
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