MolNFT v1 · #137284 · protein

De novo photosynthetic reaction center protein equipped with heme B, a synthetic zn porphyrin, and ZN(II) cations

5VJS · Reaction center maquette: “De novo photosynthetic reaction center protein equipped with heme B, a synthetic zn porphyrin, and ZN(II)…”. X-ray diffraction, 4 ligands (HEM, 9D7, ZN), 3 pockets (best druggability 0.73). MolNFT v1…

PDB: 5VJS
Type: protein
Length: 196 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reaction center maquette
Ligands: HEM, 9D7, ZN, CL
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 90% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Reaction center maquette	protein	196	90% helix, 0% strand	—

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
9D7 · [4-(15-phenylporphyrin-5-yl-kappa~4~n~21~,n~22~,n~23~, n~24~)benzoato(2-)]zinc · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
CL · Chloride ion · ion · 3 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	118	0.73	0.93	27	9D7
2	319	0.69	0.83	28	HEM
3	108	0.54	0.83	21	empty

Compared structures

5VJS · De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, a synthetic Zn… · 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 5VJS · PDBe 5VJS

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