MolNFT v1 · #157413 · protein
Room-temperature structure of deuterated tetdron (isomorph 2)
6MYC · Photoswitchable protein tetdron: “Room-temperature structure of deuterated tetdron (isomorph 2)”. X-ray diffraction, 1 ligand (GYC), 20 pockets (best druggability 0.82). MolNFT v1 #157413 on GenesisL1: 3D structure, binding sites…
- PDB
- 6MYC
- Type
- protein
- Length
- 1,711 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photoswitchable protein tetdron
- Ligands
- GYC
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H | Photoswitchable protein tetdron | protein | 214 | 3% helix, 58% strand | — |
| G | Photoswitchable protein tetdron | protein | 213 | 4% helix, 58% strand | — |
Ligands and binding sites
- GYC · [(4Z)-2-[(1R)-1-amino-2-mercaptoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.82 | 0.84 | 86 | empty |
| 2 | 70 | 0.73 | 0.98 | 23 | GYC |
| 3 | 67 | 0.73 | 0.98 | 25 | GYC |
| 4 | 64 | 0.71 | 0.97 | 26 | GYC |
| 5 | 52 | 0.71 | 0.99 | 25 | GYC |
Interfaces
11 interfaces between chains.
- B–C · 940 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 913 Ų buried · 18 hydrogen bonds · protein-protein
- F–H · 899 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 878 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 875 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 6MYC · Room-temperature structure of deuterated Tetdron (isomorph 2) · 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 6MYC · PDBe 6MYC
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