Research workbench
Cl-K1 trimer bound to MAN(ALPHA1-2)MAN
Analyse Cl-K1 trimer bound to MAN(ALPHA1-2)MAN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YMD
- Type
- protein
- Length
- 919 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collectin-11
- UniProt
- Q9BWP8
- Ligands
- MAN, CA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Collectin-11 | protein | 154 | 34% helix, 27% strand | Q9BWP8 |
| D | Collectin-11 | protein | 155 | 34% helix, 27% strand | Q9BWP8 |
| C | Collectin-11 | protein | 153 | 35% helix, 27% strand | Q9BWP8 |
| E | Collectin-11 | protein | 149 | 32% helix, 28% strand | Q9BWP8 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, D, F
- CA · Calcium ion · metal · 18 copies · chains A, B, D, F, C, E
- GOL · Glycerol · additive · 7 copies · chains A, B, D, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.81 | 0.84 | 90 | empty |
| 2 | 853 | 0.80 | 0.83 | 61 | empty |
| 3 | 151 | 0.52 | 0.80 | 24 | empty |
| 4 | 113 | 0.40 | 0.75 | 17 | empty |
| 5 | 84 | 0.37 | 0.76 | 19 | empty |
Interfaces
8 interfaces between chains.
- D–E · 857 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 781 Ų buried · 5 hydrogen bonds · protein-protein
- F–E · 723 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 715 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 698 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
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 Q9BWP8
- Elsewhere: RCSB PDB 4YMD · PDBe 4YMD · UniProt Q9BWP8
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