MolNFT v1 · #140994 · protein
Crystal structrure of near infrared fluoresecent protein MNEPTUNE684
5YT1: “Crystal structrure of near infrared fluoresecent protein MNEPTUNE684”. X-ray diffraction, 1 ligand (NRQ), 14 pockets (best druggability 0.84). MolNFT v1 #140994 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YT1
- Type
- protein
- Length
- 901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Near infrared fluoresecent protein MNEPTUNE684
- Ligands
- NRQ
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Near infrared fluoresecent protein MNEPTUNE684 | protein | 226 | 7% helix, 56% strand | — |
| B, C, D | Near infrared fluoresecent protein MNEPTUNE684 | protein | 225 | 6% helix, 56% strand | — |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.84 | 0.85 | 71 | empty |
| 2 | 88 | 0.76 | 0.98 | 26 | NRQ |
| 3 | 84 | 0.76 | 0.98 | 26 | NRQ |
| 4 | 82 | 0.74 | 0.97 | 26 | NRQ |
| 5 | 63 | 0.71 | 0.98 | 21 | NRQ |
Interfaces
6 interfaces between chains.
- A–C · 1478 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1455 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1076 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1069 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 5YT1 · Crystal structrure of near infrared fluoresecent protein mNeptune684 · 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 5YT1 · PDBe 5YT1
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