MolNFT v1 · #47919 · protein

1.8 ångström crystal structure of the CYS71SER mutant of vivid

2PD8 · Vivid pas protein vvd: “1.8 ångström crystal structure of the CYS71SER mutant of vivid”. X-ray diffraction, 1 ligand (FAD), 3 pockets (best druggability 0.73). MolNFT v1 #47919 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2PD8
Type: protein
Length: 288 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: 3 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vivid pas protein vvd	protein	148	25% helix, 26% strand	Q9C3Y6
B	Vivid pas protein vvd	protein	140	26% helix, 28% 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

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	299	0.73	0.86	35	FAD
2	235	0.72	0.87	33	FAD
3	230	0.51	0.75	34	empty

Interfaces

1 interface between chains.

A–B · 281 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2PD8 · 1.8 Angstrom Crystal Structure of the Cys71Ser mutant of 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 2PD8 · PDBe 2PD8 · UniProt Q9C3Y6

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