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Crystal structure of red fluorescent protein EQFP578 crystallized at pH 5.5
Analyse Crystal structure of red fluorescent protein EQFP578 crystallized at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PIB
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EQFP578 fluorescent protein
- Ligands
- NRQ
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EQFP578 fluorescent protein | protein | 226 | 6% helix, 56% strand | — |
| B | EQFP578 fluorescent protein | protein | 235 | 7% helix, 54% strand | — |
| C | EQFP578 fluorescent protein | protein | 225 | 6% helix, 56% strand | — |
| D | EQFP578 fluorescent protein | protein | 227 | 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
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.82 | 0.83 | 68 | empty |
| 2 | 79 | 0.76 | 0.99 | 25 | NRQ, GOL |
| 3 | 79 | 0.75 | 0.98 | 21 | NRQ |
| 4 | 82 | 0.75 | 0.98 | 24 | NRQ, GOL |
| 5 | 82 | 0.74 | 0.98 | 20 | NRQ, GOL |
Interfaces
6 interfaces between chains.
- B–C · 1692 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1654 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1119 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1080 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 38 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 3PIB · Crystal structure of red fluorescent protein eqFP578 crystallized at pH 5.5 · 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 3PIB · PDBe 3PIB
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