Research workbench
Crystal structure of blue fluorescent protein from metagenomic library in complex with NADPH
Analyse Crystal structure of blue fluorescent protein from metagenomic library in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J7U
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blue fluorescent protein
- EC
- 1.2.4.4
- UniProt
- D6NKF4
- Ligands
- NDP
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Blue fluorescent protein (EC 1.2.4.4) | protein | 247 | 47% helix, 15% strand | D6NKF4 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.85 | 0.86 | 70 | empty |
| 2 | 1072 | 0.83 | 0.84 | 109 | NDP |
| 3 | 1016 | 0.83 | 0.84 | 106 | NDP |
| 4 | 154 | 0.51 | 0.79 | 20 | empty |
| 5 | 142 | 0.48 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1645 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1640 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1599 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1593 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 243 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6J7U · Crystal structure of blue fluorescent protein from metagenomic library in complex with… · 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
- Every structure of UniProt D6NKF4
- Elsewhere: RCSB PDB 6J7U · PDBe 6J7U · UniProt D6NKF4
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