MolNFT v1 · #47918 · protein

2.0 ångström crystal structure of the fungal blue-light photoreceptor vivid

2PD7 · Vivid pas protein vvd: “2.0 ångström crystal structure of the fungal blue-light photoreceptor vivid”. X-ray diffraction, 1 ligand (FAD), 4 pockets (best druggability 0.72). MolNFT v1 #47918 on GenesisL1: 3D structure, binding sites…

PDB: 2PD7
Type: protein
Length: 291 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vivid pas protein vvd
UniProt: Q9C3Y6
Ligands: FAD
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vivid pas protein vvd	protein	149	25% helix, 26% strand	Q9C3Y6
B	Vivid pas protein vvd	protein	142	26% helix, 27% strand	Q9C3Y6

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B

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	245	0.72	0.87	31	FAD
2	236	0.71	0.87	31	FAD
3	84	0.36	0.76	18	empty
4	54	0.25	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 437 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2PD7 · 2.0 Angstrom Crystal Structure of the Fungal Blue-Light Photoreceptor Vivid · 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 Q9C3Y6
Elsewhere: RCSB PDB 2PD7 · PDBe 2PD7 · UniProt Q9C3Y6

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