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Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A198L variant

Analyse Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A198L variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6H7R
Type: protein
Length: 1,172 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.8
Source: Sulfolobus solfataricus
Molecule: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
EC: 4.1.2.55
UniProt: O54288
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · resolution 2.8 · 1 distinct chain · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase (EC 4.1.2.55)	protein	293	52% helix, 14% strand	O54288

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, C

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	302	0.74	0.86	46	empty
2	343	0.73	0.85	39	GOL
3	419	0.73	0.83	50	empty
4	336	0.73	0.85	36	empty
5	287	0.72	0.86	37	empty

Interfaces

4 interfaces between chains.

C–D · 1685 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1625 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1135 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1094 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6H7R · Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A198L variant · the same entry in another collection · chain A against A, TM-score 1.00
O54288 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxy… · a predicted model of the same protein · chain A 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 O54288
Elsewhere: RCSB PDB 6H7R · PDBe 6H7R · UniProt O54288

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