MolNFT v1 · #126143 · protein

GMHA_MUTANT Q175E

5LTZ · Phosphoheptose isomerase: “GMHA_MUTANT Q175E”. X-ray diffraction, 3 ligands (I22, ZN, NA), 8 pockets (best druggability 0.72). MolNFT v1 #126143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LTZ
Type: protein
Length: 774 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: I22, ZN, NA
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 59% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Phosphoheptose isomerase (EC 5.3.1.28)	protein	193	59% helix, 11% strand	Q93UJ2
D	Phosphoheptose isomerase (EC 5.3.1.28)	protein	195	58% helix, 11% strand	Q93UJ2

Ligands and binding sites

I22 · D-altro-hept-2-ulose 7-phosphate · ligand · 4 copies · chains A, B, D, C
ZN · Zinc ion · metal · 4 copies · chains A, D, B, C
NA · Sodium ion · metal
PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, D
EDO · 1,2-ethanediol · additive · chains B
PGE · Triethylene glycol · additive · chains C
PEG · Di(hydroxyethyl)ether · additive · chains D
GOL · Glycerol · additive · chains B, D

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	52	0.72	0.99	21	empty
2	147	0.61	0.85	28	I22
3	161	0.60	0.83	30	I22
4	218	0.59	0.81	50	I22
5	153	0.59	0.84	24	I22

Interfaces

6 interfaces between chains.

A–D · 1759 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1751 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 1237 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1222 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 704 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5LTZ · GmhA_mutant Q175E · 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 5LTZ · PDBe 5LTZ · UniProt Q93UJ2

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