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Crystal structure of the blue fluorescent protein with a leu-leu-gly tri-peptide chromophore derived from the purple chromoprotein of stichodactyla haddoni

Analyse Crystal structure of the blue fluorescent protein with a leu-leu-gly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JC5
Type: protein
Length: 1,757 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Shbfp
Ligands: BJF
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, G	Shbfp	protein	220	6% helix, 56% strand	—
E, F, H	Shbfp	protein	219	6% helix, 57% strand	—

Ligands and binding sites

BJF · {2-[(1S)-1-amino-3-methylbutyl]-5-hydroxy-4-(2-methylpropyl)-1H-imidazol-1-yl}acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1008	0.83	0.84	94	empty
2	1090	0.82	0.84	93	empty
3	94	0.78	0.98	26	BJF
4	93	0.77	0.98	29	BJF
5	89	0.77	0.98	25	BJF

Interfaces

13 interfaces between chains.

F–H · 1597 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1527 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 1515 Å² buried · 19 hydrogen bonds · protein-protein
E–G · 1478 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 846 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 covalent (covalent ligand).

Compared structures

6JC5 · Crystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide… · 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 6JC5 · PDBe 6JC5

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