Research workbench

PSF4 in complex with MN2+ and (S)-2-hpp

Analyse PSF4 in complex with MN2+ and (S)-2-hpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U55
Type: protein
Length: 745 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: (S)-2-hydroxypropylphosphonic acid epoxidase
EC: 1.11.1.23
UniProt: Q9JN69
Ligands: S0H, MN
Pockets: 13 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	(S)-2-hydroxypropylphosphonic acid epoxidase (EC 1.11.1.23)	protein	187	17% helix, 39% strand	Q9JN69
B, C, D	(S)-2-hydroxypropylphosphonic acid epoxidase (EC 1.11.1.23)	protein	186	17% helix, 40% strand	Q9JN69

Ligands and binding sites

S0H · (S)-2-hydroxypropylphosphonic acid · ligand · 4 copies · chains A, D, B, C
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	69	0.45	0.82	23	MN, S0H
2	101	0.41	0.77	19	empty
3	107	0.38	0.75	24	empty
4	111	0.37	0.75	23	empty
5	99	0.36	0.75	24	empty

Interfaces

4 interfaces between chains.

A–C · 1849 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 1840 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 1459 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1353 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5U55 · Psf4 in complex with Mn2+ and (S)-2-HPP · the same entry in another collection · chain A against A, TM-score 1.00
Q9JN69 · AlphaFold monomer V2.0 prediction for (S)-2-hydroxypropylphosphonic acid epoxidase… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9JN69
Elsewhere: RCSB PDB 5U55 · PDBe 5U55 · UniProt Q9JN69

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