MolNFT v1 · #47440 · protein

Crystal structure of cdp-bound protein MJ0056 from methanococcus jannaschii, pfam DUF120

2OYN · Hypothetical protein MJ0056: “Crystal structure of cdp-bound protein MJ0056 from methanococcus jannaschii, pfam DUF120”. X-ray diffraction, 2 ligands (CDP, NA), 3 pockets (best druggability 0.55). MolNFT v1 #47440 on GenesisL1: 3D…

PDB: 2OYN
Type: protein
Length: 137 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein MJ0056
UniProt: Q60365
Ligands: CDP, NA
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein MJ0056	protein	137	18% helix, 44% strand	Q60365

Ligands and binding sites

CDP · Cytidine-5'-diphosphate · ligand · chains A
NA · Sodium ion · metal · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	138	0.55	0.82	22	NA, CDP
2	112	0.50	0.80	18	empty
3	95	0.43	0.78	17	empty

Compared structures

2OYN · Crystal structure of CDP-bound protein MJ0056 from Methanococcus jannaschii, Pfam DUF120 · the same entry in another collection · chain A against A, TM-score 1.00
Q60365 · AlphaFold monomer V2.0 prediction for riboflavin kinase (Q60365) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q60365
Elsewhere: RCSB PDB 2OYN · PDBe 2OYN · UniProt Q60365

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