MolNFT v1 · #111680 · protein
Computationally designed left-handed ALPHA/ALPHA toroid with 3 repeats in space group P212121
4YY2 · DTOR_3X33L: “Computationally designed left-handed ALPHA/ALPHA toroid with 3 repeats in space group P212121”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.71). MolNFT v1 #111680 on GenesisL1: 3D structure, binding…
- PDB
- 4YY2
- Type
- protein
- Length
- 395 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DTOR_3X33L
- Ligands
- NA
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | DTOR_3X33L | protein | 99 | 78% helix, 0% strand | — |
| C | DTOR_3X33L | protein | 98 | 79% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.71 | 0.76 | 61 | empty |
| 2 | 289 | 0.63 | 0.80 | 31 | NA |
| 3 | 107 | 0.51 | 0.82 | 21 | empty |
| 4 | 79 | 0.38 | 0.77 | 15 | NA |
Interfaces
5 interfaces between chains.
- A–B · 506 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 116 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YY2 · Computationally designed left-handed alpha/alpha toroid with 3 repeats in space group… · the same entry in another collection · chain C against C, 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 4YY2 · PDBe 4YY2
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