MolNFT v1 · #51535 · protein

Monomeric red fluorescent protein, DSRED.M1

2VAD: “Monomeric red fluorescent protein, DSRED.M1”. X-ray diffraction, 3 ligands (CRQ, ZN, CL), 2 pockets (best druggability 0.77). MolNFT v1 #51535 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VAD
Type: protein
Length: 217 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Red fluorescent protein
Ligands: CRQ, ZN, CL
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Red fluorescent protein	protein	217	6% helix, 57% strand	—

Ligands and binding sites

CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · chains A
ZN · Zinc ion · metal · 3 copies · chains A
CL · Chloride ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	91	0.77	0.98	27	CRQ
2	74	0.42	0.80	20	empty

Modifications

Observed in the structure: 2 cofactor (chromophore).

Compared structures

2VAD · Monomeric red fluorescent protein, DsRed.M1 · 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 2VAD · PDBe 2VAD

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