MolNFT v1 · #141094 · protein

Crystal structure of the kdo hydroxylase kdoo, a non-heme FE(II) alphaketoglutarate dependent dioxygenase in complex with succinate and FE(III)

5YW0 · Uncharacterized protein kdoo: “Crystal structure of the kdo hydroxylase kdoo, a non-heme FE(II) alphaketoglutarate dependent dioxygenase in…”. X-ray diffraction, 1 ligand (FE), 2 pockets (best druggability 0.63). MolNFT v1 #141094…

PDB: 5YW0
Type: protein
Length: 293 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein kdoo
UniProt: B3DUR4
Ligands: FE
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein kdoo	protein	293	36% helix, 20% strand	B3DUR4

Ligands and binding sites

FE · Fe (III) ion · metal · chains A
PG4 · Tetraethylene glycol · additive · 5 copies · chains A
ACT · Acetate ion · additive · 4 copies · chains A
GOL · Glycerol · additive · chains A
SIN · Succinic acid · additive · chains A

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

Pockets

2 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	422	0.63	0.77	47	PG4, FE, SIN, ACT
2	53	0.29	0.75	13	ACT

Compared structures

5YW0 · Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate… · 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 B3DUR4
Elsewhere: RCSB PDB 5YW0 · PDBe 5YW0 · UniProt B3DUR4

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