MolNFT v1 · #181353 · protein
Crystal structure of near-infrared fluorescent protein MIRFP718NANO
7LSD: “Crystal structure of near-infrared fluorescent protein MIRFP718NANO”. X-ray diffraction, 1 ligand (BLA), 8 pockets (best druggability 0.69). MolNFT v1 #181353 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LSD
- Type
- protein
- Length
- 605 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MIRFP718NANO
- Ligands
- BLA
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MIRFP718NANO | protein | 151 | 38% helix, 26% strand | — |
| B, C | MIRFP718NANO | protein | 152 | 41% helix, 26% strand | — |
| D | MIRFP718NANO | protein | 150 | 41% helix, 26% strand | — |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.69 | 0.88 | 30 | BLA |
| 2 | 150 | 0.66 | 0.87 | 27 | BLA |
| 3 | 131 | 0.65 | 0.87 | 21 | BLA |
| 4 | 164 | 0.64 | 0.84 | 30 | BLA |
| 5 | 60 | 0.31 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1004 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 997 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (biliverdin attachment).
Compared structures
- 7LSD · Crystal structure of near-infrared fluorescent protein miRFP718nano · 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 7LSD · PDBe 7LSD
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