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Heptose isomerase gmha mutant - D61A

Analyse Heptose isomerase gmha mutant - D61A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LU7
Type: protein
Length: 776 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoheptose isomerase
EC: 5.3.1.28
UniProt: Q93UJ2
Ligands: M7P, ZN
Pockets: 12 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Phosphoheptose isomerase (EC 5.3.1.28)	protein	193	60% helix, 11% strand	Q93UJ2
D	Phosphoheptose isomerase (EC 5.3.1.28)	protein	197	60% helix, 11% strand	Q93UJ2

Ligands and binding sites

M7P · 7-O-phosphono-D-glycero-alpha-D-manno-heptopyranose · ligand · 4 copies · chains A, B, D, C
ZN · Zinc ion · metal · 4 copies · chains A, D, B, C
PG4 · Tetraethylene glycol · additive · 3 copies · chains A, C
EDO · 1,2-ethanediol · additive · 2 copies · chains C

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.72	0.98	23	empty
2	55	0.72	0.98	25	empty
3	55	0.71	0.98	22	empty
4	56	0.69	0.97	22	empty
5	222	0.61	0.82	38	M7P

Interfaces

6 interfaces between chains.

A–D · 1796 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1784 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1217 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 1200 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 703 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5LU7 · Heptose isomerase GmhA mutant - D61A · the same entry in another collection · chain A against A, TM-score 1.00
Q93UJ2 · AlphaFold monomer V2.0 prediction for phosphoheptose isomerase (Q93UJ2) · a predicted model of the same protein · 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 Q93UJ2
Elsewhere: RCSB PDB 5LU7 · PDBe 5LU7 · UniProt Q93UJ2

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