MolNFT v1 · #177932 · protein

FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase sptf with terretonin C

7EYW · 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase sptf with terretonin C”. X-ray diffraction, 3 ligands (OGA, 0IP, FE2), 16 pockets (best druggability 0.76). MolNFT v1 #177932 on…

PDB: 7EYW
Type: protein
Length: 1,058 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf
UniProt: A0A6J4CX17
Ligands: OGA, 0IP, FE2
Pockets: 16 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf	protein	277	29% helix, 18% strand	A0A6J4CX17
A	2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf	protein	271	31% helix, 18% strand	A0A6J4CX17
B	2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf	protein	258	31% helix, 20% strand	A0A6J4CX17
D	2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf	protein	252	31% helix, 21% strand	A0A6J4CX17

Ligands and binding sites

OGA · N-oxalylglycine · ligand · 4 copies · chains C, A, B, D
0IP · Terretonin C · ligand · chains B
FE2 · Fe (II) ion · metal · 4 copies · chains C, A, B, D

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

Pockets

16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	843	0.76	0.80	92	empty
2	214	0.55	0.78	28	OGA, FE2
3	191	0.52	0.78	29	OGA, FE2, 0IP
4	179	0.52	0.78	29	OGA
5	190	0.50	0.77	28	OGA, FE2

Interfaces

5 interfaces between chains.

C–A · 879 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 509 Å² buried · 1 hydrogen bond · protein-protein
C–B · 377 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 155 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 31 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7EYW · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with terretonin C · the same entry in another collection · chain C against C, 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 A0A6J4CX17
Elsewhere: RCSB PDB 7EYW · PDBe 7EYW · UniProt A0A6J4CX17

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