MolNFT v1 · #116350 · protein

FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase asqj in complex with cyclopeptin

5DAW · Phytanoyl-CoA dioxygenase family protein (AFU_ORTHOLOGUE…: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase asqj in complex with cyclopeptin”. X-ray diffraction, 3 ligands (AKG, 58K, NI), 3 pockets (best druggability 0.73). MolNFT…

PDB: 5DAW
Type: protein
Length: 288 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phytanoyl-CoA dioxygenase family protein (AFU_ORTHOLOGUE AFUA_8G00230)
UniProt: Q5AR53
Ligands: AKG, 58K, NI
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phytanoyl-CoA dioxygenase family protein (AFU_ORTHOLOGUE AFUA_8G00230)	protein	288	25% helix, 21% strand	Q5AR53

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · chains A
58K · cyclopeptin · ligand · chains A
NI · Nickel (II) 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	429	0.73	0.83	51	NI, AKG, 58K
2	165	0.55	0.81	27	empty
3	58	0.30	0.75	14	empty

Compared structures

Q5AR53 · AlphaFold monomer V2.0 prediction for IRON/ALPHA-ketoglutarate- dependent dioxygenase… · a predicted model of the same protein · 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 Q5AR53
Elsewhere: RCSB PDB 5DAW · PDBe 5DAW · UniProt Q5AR53

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