MolNFT v1 · #137454 · protein
Light-sensitive photoprotein
5VP3 · Mnemiopsin 1: “Light-sensitive photoprotein”. X-ray diffraction, 3 ligands (CD, NI, SCN), 2 pockets (best druggability 0.47). MolNFT v1 #137454 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VP3
- Type
- protein
- Length
- 195 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mnemiopsin 1
- UniProt
- E0WVU4
- Ligands
- CD, NI, SCN
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mnemiopsin 1 | protein | 195 | 62% helix, 4% strand | E0WVU4 |
Ligands and binding sites
- CD · Cadmium ion · metal · 4 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- SCN · Thiocyanate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.47 | 0.76 | 20 | empty |
| 2 | 51 | 0.39 | 0.81 | 12 | empty |
Compared structures
- 5VP3 · Light-sensitive photoprotein · 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 E0WVU4
- Elsewhere: RCSB PDB 5VP3 · PDBe 5VP3 · UniProt E0WVU4
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