MolNFT v1 · #145432 · protein

2.3 ångström structure of phosphodiesterase treated vivid (complex with FMN)

6CNY · Vivid pas protein vvd: “2.3 ångström structure of phosphodiesterase treated vivid (complex with FMN)”. X-ray diffraction, 1 ligand (FMN), 8 pockets (best druggability 0.73). MolNFT v1 #145432 on GenesisL1: 3D structure, binding…

PDB: 6CNY
Type: protein
Length: 578 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vivid pas protein vvd
UniProt: Q9C3Y6
Ligands: FMN
Pockets: 8 · best druggability 0.73

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Vivid pas protein vvd	protein	147	26% helix, 27% strand	Q9C3Y6
B, D	Vivid pas protein vvd	protein	142	27% helix, 27% strand	Q9C3Y6

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	208	0.73	0.89	26	FMN
2	214	0.73	0.89	33	FMN
3	217	0.73	0.88	27	FMN
4	217	0.72	0.88	34	FMN
5	167	0.45	0.75	19	empty

Interfaces

3 interfaces between chains.

C–D · 439 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 435 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 342 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

6CNY · 2.3 Angstrom Structure of Phosphodiesterase treated Vivid (complex with FMN) · 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 6CNY · PDBe 6CNY · UniProt Q9C3Y6

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