MolNFT v1 · #176442 · protein
Photocleavable fluorescent protein in green form
7DMX · Phocl green: “Photocleavable fluorescent protein in green form”. X-ray diffraction, 1 ligand (CR8), 15 pockets (best druggability 0.75). MolNFT v1 #176442 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DMX
- Type
- protein
- Length
- 841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phocl green
- Ligands
- CR8
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phocl green | protein | 210 | 3% helix, 59% strand | — |
| B | Phocl green | protein | 209 | 3% helix, 59% strand | — |
| C | Phocl green | protein | 207 | 3% helix, 59% strand | — |
| D | Phocl green | protein | 215 | 3% helix, 57% strand | — |
Ligands and binding sites
- CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.75 | 0.98 | 28 | CR8 |
| 2 | 97 | 0.75 | 0.97 | 28 | CR8 |
| 3 | 87 | 0.74 | 0.97 | 26 | CR8 |
| 4 | 84 | 0.74 | 0.97 | 29 | CR8 |
| 5 | 332 | 0.56 | 0.76 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–B · 960 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 944 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 228 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 226 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7DMX · Photocleavable Fluorescent Protein in green form · 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 7DMX · PDBe 7DMX
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