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Crystal structure of yghz from E. COLI

Analyse Crystal structure of yghz from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3N6Q
Type: protein
Length: 2,498 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yghz aldo-keto reductase
UniProt: Q46851
Ligands: MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yghz aldo-keto reductase	protein	314	44% helix, 15% strand	Q46851
B	Yghz aldo-keto reductase	protein	315	42% helix, 15% strand	Q46851
C, F, G	Yghz aldo-keto reductase	protein	313	43% helix, 15% strand	Q46851
D	Yghz aldo-keto reductase	protein	315	43% helix, 15% strand	Q46851
E	Yghz aldo-keto reductase	protein	309	42% helix, 15% strand	Q46851
H	Yghz aldo-keto reductase	protein	306	41% helix, 15% strand	Q46851

Ligands and binding sites

MG · Magnesium ion · metal · 9 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1004	0.84	0.85	134	empty
2	976	0.84	0.85	115	empty
3	428	0.63	0.77	54	empty
4	178	0.57	0.81	30	empty
5	142	0.57	0.83	23	empty

Interfaces

12 interfaces between chains.

F–G · 949 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 945 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 942 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 937 Å² buried · 12 hydrogen bonds · protein-protein
E–H · 936 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3N6Q · Crystal structure of YghZ from E. coli · the same entry in another collection · chain H against H, TM-score 1.00
Q46851 · AlphaFold monomer V2.0 prediction for L-glyceraldehyde 3-phosphate reductase (Q46851) · a predicted model of the same protein · chain H 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 Q46851
Elsewhere: RCSB PDB 3N6Q · PDBe 3N6Q · UniProt Q46851

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