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Proline hydroxylase H11-N101I mutant

Analyse Proline hydroxylase H11-N101I mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DT0
Type: protein
Length: 1,958 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phytanoyl-CoA dioxygenase
UniProt: S5TUM1
Ligands: AKG, PRO, FE
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 8 distinct chains · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phytanoyl-CoA dioxygenase	protein	253	30% helix, 23% strand	S5TUM1
B	Phytanoyl-CoA dioxygenase	protein	244	29% helix, 24% strand	S5TUM1
C	Phytanoyl-CoA dioxygenase	protein	242	29% helix, 23% strand	S5TUM1
D	Phytanoyl-CoA dioxygenase	protein	243	27% helix, 22% strand	S5TUM1
E	Phytanoyl-CoA dioxygenase	protein	246	28% helix, 22% strand	S5TUM1
F	Phytanoyl-CoA dioxygenase	protein	245	31% helix, 24% strand	S5TUM1
G	Phytanoyl-CoA dioxygenase	protein	244	27% helix, 23% strand	S5TUM1
H	Phytanoyl-CoA dioxygenase	protein	241	26% helix, 24% strand	S5TUM1

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
PRO · Proline · ligand · 8 copies · chains A, B, C, D, E, F, G, H
FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	655	0.78	0.83	52	AKG, PRO
2	611	0.75	0.82	42	AKG, PRO, FE
3	565	0.73	0.81	47	AKG, FE, PRO
4	54	0.73	0.99	17	empty
5	58	0.72	0.98	18	empty

Interfaces

10 interfaces between chains.

B–E · 1077 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 1038 Å² buried · 6 hydrogen bonds · protein-protein
F–G · 1034 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 319 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 308 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7DT0 · Proline hydroxylase H11-N101I mutant · 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 7DT0 · PDBe 7DT0 · UniProt S5TUM1

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