MolNFT v1 · #186544 · protein

A new fluorescent protein darkmruby at pH 9.0

7RHC: “A new fluorescent protein darkmruby at pH 9.0”. X-ray diffraction, 1 ligand (NRQ), 4 pockets (best druggability 0.74). MolNFT v1 #186544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7RHC
Type: protein
Length: 437 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Darkmruby
Ligands: NRQ
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Darkmruby	protein	218	4% helix, 58% strand	—
A	Darkmruby	protein	219	3% helix, 58% 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 · 2 copies · chains B, A
EDO · 1,2-ethanediol · additive · 4 copies · chains B, A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.74	0.98	29	NRQ
2	67	0.72	0.97	26	NRQ
3	60	0.28	0.74	18	empty
4	55	0.26	0.73	18	empty

Interfaces

1 interface between chains.

B–A · 990 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

7RHC · A new fluorescent protein darkmRuby at pH 9.0 · the same entry in another collection · chain B against B, 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 7RHC · PDBe 7RHC

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