MolNFT v1 · #176866 · protein

Trans-3/4-proline-hydroxylase H11 with akg

7E06 · Phytanoyl-CoA dioxygenase: “Trans-3/4-proline-hydroxylase H11 with akg”. X-ray diffraction, 2 ligands (AKG, FE), 9 pockets (best druggability 0.69). MolNFT v1 #176866 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7E06
Type: protein
Length: 512 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phytanoyl-CoA dioxygenase
UniProt: S5TUM1
Ligands: AKG, FE
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phytanoyl-CoA dioxygenase	protein	251	27% helix, 23% strand	S5TUM1
B	Phytanoyl-CoA dioxygenase	protein	261	26% helix, 21% strand	S5TUM1

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
FE · Fe (III) ion · metal · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	276	0.69	0.84	43	AKG, FE
2	223	0.62	0.82	27	empty
3	192	0.51	0.77	23	empty
4	187	0.51	0.77	23	empty
5	54	0.37	0.80	14	empty

Interfaces

1 interface between chains.

A–B · 827 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

7E06 · Trans-3/4-proline-hydroxylase H11 with AKG · 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 S5TUM1
Elsewhere: RCSB PDB 7E06 · PDBe 7E06 · UniProt S5TUM1

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