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The crystal structure of D-psicose-3-epimerase from biortus.

Analyse The crystal structure of D-psicose-3-epimerase from biortus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E9W
Type: protein
Length: 1,160 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-psicose 3-epimerase
EC: 5.1.3.30
UniProt: B8I944
Ligands: MN
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	D-psicose 3-epimerase (EC 5.1.3.30)	protein	290	48% helix, 13% strand	B8I944

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 12 copies · chains A, D, B, C

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	965	0.86	0.87	73	empty
2	115	0.73	0.93	25	GOL
3	119	0.71	0.92	26	GOL
4	778	0.71	0.77	87	GOL
5	136	0.68	0.89	32	GOL

Interfaces

6 interfaces between chains.

A–D · 1456 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 1443 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 635 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 631 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 205 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7E9W · The Crystal Structure of D-psicose-3-epimerase from Biortus. · the same entry in another collection · chain D against D, TM-score 1.00
B8I944 · AlphaFold monomer V2.0 prediction for D-psicose 3-epimerase (B8I944) · a predicted model of the same protein · chain D 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 B8I944
Elsewhere: RCSB PDB 7E9W · PDBe 7E9W · UniProt B8I944

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