MolNFT v1 · #181352 · protein
Crystal structure of near-infrared fluorescent protein MIRFP670NANO3
7LSC: “Crystal structure of near-infrared fluorescent protein MIRFP670NANO3”. X-ray diffraction, 1 ligand (JRA), 8 pockets (best druggability 0.78). MolNFT v1 #181352 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LSC
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MIRFP670NANO3
- Ligands
- JRA
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MIRFP670NANO3 | protein | 161 | 37% helix, 24% strand | — |
| B | MIRFP670NANO3 | protein | 147 | 37% helix, 27% strand | — |
| C | MIRFP670NANO3 | protein | 151 | 38% helix, 26% strand | — |
| D | MIRFP670NANO3 | protein | 145 | 38% helix, 27% strand | — |
Ligands and binding sites
- JRA · 3-[2-[(~{Z})-[5-[(~{Z})-[(3~{S},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.78 | 0.82 | 81 | JRA |
| 2 | 753 | 0.78 | 0.81 | 80 | JRA |
| 3 | 100 | 0.76 | 0.97 | 20 | empty |
| 4 | 91 | 0.76 | 0.97 | 21 | empty |
| 5 | 480 | 0.64 | 0.77 | 49 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1212 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 791 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 530 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7LSC · Crystal structure of near-infrared fluorescent protein miRFP670nano3 · 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 7LSC · PDBe 7LSC
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