MolNFT v1 · #89038 · protein
Computationally designed self-assembling octahedral cage protein, O333, crystallized in space group P4
4DDF · Propanediol utilization polyhedral body protein pdut: “Computationally designed self-assembling octahedral cage protein, O333, crystallized in space group P4”. X-ray diffraction, 2 ligands (SO4, CL), 19 pockets (best druggability…
- PDB
- 4DDF
- Type
- protein
- Length
- 2,196 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propanediol utilization polyhedral body protein pdut
- UniProt
- E7V033
- Ligands
- SO4, CL
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Propanediol utilization polyhedral body protein pdut | protein | 183 | 42% helix, 34% strand | E7V033 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, G, H, I, J, K, L
- CL · Chloride ion · ion · 12 copies · chains A, B, C, J, E, F, G, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.75 | 0.85 | 59 | CL |
| 2 | 635 | 0.69 | 0.77 | 40 | empty |
| 3 | 67 | 0.63 | 0.92 | 21 | empty |
| 4 | 311 | 0.59 | 0.77 | 25 | empty |
| 5 | 224 | 0.55 | 0.78 | 25 | empty |
Interfaces
23 interfaces between chains.
- A–C · 826 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 824 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 820 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 814 Ų buried · 15 hydrogen bonds · protein-protein
- G–I · 804 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4DDF · Computationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in… · 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 E7V033
- Elsewhere: RCSB PDB 4DDF · PDBe 4DDF · UniProt E7V033
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