MolNFT v1 · #25703 · protein

2-keto-3-DEOXYGLUCONATE(KDG) aldolase of sulfolobus solfataricus

1W37 · 2-keto-3-deoxy gluconate aldolase: “2-keto-3-DEOXYGLUCONATE(KDG) aldolase of sulfolobus solfataricus”. X-ray diffraction, 1 ligand (NA), 14 pockets (best druggability 0.75). MolNFT v1 #25703 on GenesisL1: 3D structure, binding sites…

PDB: 1W37
Type: protein
Length: 1,172 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-keto-3-deoxy gluconate aldolase
EC: 4.1.2.20
UniProt: O54288
Ligands: NA
Pockets: 14 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	2-keto-3-deoxy gluconate aldolase (EC 4.1.2.20)	protein	293	53% helix, 14% strand	O54288

Ligands and binding sites

NA · Sodium ion · metal · chains D
GOL · Glycerol · additive · 8 copies · chains A, D, B, C

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

Pockets

14 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	257	0.75	0.89	33	empty
2	227	0.75	0.89	29	empty
3	276	0.75	0.88	38	GOL
4	277	0.73	0.87	40	empty
5	311	0.73	0.85	38	GOL

Interfaces

4 interfaces between chains.

B–C · 1765 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1711 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1136 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1133 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1W37 · 2-keto-3-deoxygluconate(KDG) aldolase of Sulfolobus solfataricus · 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 1W37 · PDBe 1W37 · UniProt O54288

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