MolNFT v1 · #83626 · protein
Crystal structure of a prostate-specific WGA16 glycoprotein lectin, form II
3WOC · Hypothetical protein: “Crystal structure of a prostate-specific WGA16 glycoprotein lectin, form II”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.77). MolNFT v1 #83626 on GenesisL1: 3D structure, binding sites…
- PDB
- 3WOC
- Type
- protein
- Length
- 824 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Hypothetical protein | protein | 138 | 0% helix, 57% strand | — |
| B, C, E, F | Hypothetical protein | protein | 137 | 0% helix, 57% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
- DIO · 1,4-diethylene dioxide · additive · 16 copies · chains A, E, C, B, D, F
- GOL · Glycerol · additive · 2 copies · chains A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.77 | 1.00 | 19 | empty |
| 2 | 54 | 0.75 | 1.00 | 19 | empty |
| 3 | 1159 | 0.73 | 0.76 | 113 | DIO, GOL, SO4 |
| 4 | 103 | 0.72 | 0.94 | 22 | empty |
| 5 | 274 | 0.72 | 0.86 | 39 | DIO |
Interfaces
7 interfaces between chains.
- C–F · 851 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 811 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 480 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 401 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 299 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3WOC · Crystal structure of a prostate-specific WGA16 glycoprotein lectin, form II · 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 3WOC · PDBe 3WOC
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