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Crystal structure of fluorescent protein unag N57A mutant
Analyse Crystal structure of fluorescent protein unag N57A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I3D
- Type
- protein
- Length
- 556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bilirubin-inducible fluorescent protein unag
- UniProt
- P0DM59
- Ligands
- BLR
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bilirubin-inducible fluorescent protein unag | protein | 139 | 12% helix, 53% strand | P0DM59 |
Ligands and binding sites
- BLR · 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-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
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.87 | 0.90 | 69 | BLR |
| 2 | 622 | 0.86 | 0.91 | 63 | BLR |
| 3 | 478 | 0.86 | 0.92 | 47 | BLR |
| 4 | 404 | 0.84 | 0.92 | 41 | BLR |
| 5 | 132 | 0.57 | 0.83 | 31 | empty |
Interfaces
4 interfaces between chains.
- B–D · 464 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 293 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 150 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4I3D · Crystal structure of fluorescent protein UnaG N57A mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P0DM59 · AlphaFold monomer V2.0 prediction for bilirubin-inducible fluorescent protein unag… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P0DM59
- Elsewhere: RCSB PDB 4I3D · PDBe 4I3D · UniProt P0DM59
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