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Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant

Analyse Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GSO
Type: protein
Length: 1,172 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-dehydro-3-deoxy-PHOSPHOGLUCONATE/2-dehydro-3-deoxy-6- phosphogalactonate aldolase
EC: 4.1.2.55
UniProt: O54288
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 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

EDO · 1,2-ethanediol · additive · 3 copies · chains C, D
GOL · Glycerol · additive · 2 copies · chains C, D

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

Pockets

12 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	306	0.78	0.89	33	empty
2	372	0.74	0.85	35	empty
3	405	0.73	0.84	42	empty
4	288	0.73	0.86	38	empty
5	338	0.73	0.85	33	empty

Interfaces

4 interfaces between chains.

A–B · 1723 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1656 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1130 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1099 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6GSO · Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C 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 6GSO · PDBe 6GSO · UniProt O54288

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