Research workbench

FT_5 dioxygenase apoenzyme

Analyse FT_5 dioxygenase apoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6D1O
Type: protein
Length: 2,137 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase
EC: 1.14.11.44
UniProt: Q8KSC8
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 8 distinct chains · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	(R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44)	protein	264	24% helix, 28% strand	Q8KSC8
B	(R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44)	protein	263	24% helix, 28% strand	Q8KSC8
C	(R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44)	protein	266	24% helix, 28% strand	Q8KSC8
D	(R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44)	protein	265	24% helix, 28% strand	Q8KSC8
E	(R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44)	protein	266	24% helix, 27% strand	Q8KSC8
F	(R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44)	protein	262	24% helix, 28% strand	Q8KSC8
G	(R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44)	protein	275	23% helix, 30% strand	Q8KSC8
H	(R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44)	protein	276	23% helix, 30% strand	Q8KSC8

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.80	0.81	105	empty
2	523	0.71	0.80	50	empty
3	661	0.68	0.76	61	empty
4	455	0.68	0.79	42	empty
5	645	0.66	0.75	54	empty

Interfaces

15 interfaces between chains.

E–H · 1009 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 943 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 891 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 873 Å² buried · 13 hydrogen bonds · protein-protein
D–H · 809 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6D1O · FT_5 dioxygenase apoenzyme · the same entry in another collection · chain H against H, TM-score 1.00
Q8KSC8 · AlphaFold monomer V2.0 prediction for (R)-PHENOXYPROPIONATE/ALPHA… · a predicted model of the same protein · chain F against A, TM-score 0.99

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 Q8KSC8
Elsewhere: RCSB PDB 6D1O · PDBe 6D1O · UniProt Q8KSC8

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