MolNFT v1 · #83169 · protein
Crystal structure of ding protein
3W9W: “Crystal structure of ding protein”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.67). MolNFT v1 #83169 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3W9W
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ding protein
- UniProt
- P85173
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ding protein | protein | 376 | 34% helix, 18% strand | P85173 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.67 | 0.75 | 82 | empty |
| 2 | 281 | 0.52 | 0.75 | 37 | GOL |
| 3 | 90 | 0.38 | 0.76 | 21 | empty |
| 4 | 71 | 0.34 | 0.76 | 20 | empty |
| 5 | 66 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 P85173
- Elsewhere: RCSB PDB 3W9W · PDBe 3W9W · UniProt P85173
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