MolNFT v1 · #108127 · protein

2-keto 3-deoxygluconate aldolase from picrophilus torridus

4UXD · 2-dehydro-3-deoxy-D-GLUCONATE/2-dehydro-3-deoxy…: “2-keto 3-deoxygluconate aldolase from picrophilus torridus”. X-ray diffraction, 9 pockets (best druggability 0.74). MolNFT v1 #108127 on GenesisL1: 3D structure, binding sites and…

PDB: 4UXD
Type: protein
Length: 1,096 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-dehydro-3-deoxy-D-GLUCONATE/2-dehydro-3-deoxy- phosphogluconate aldolase
EC: 4.1.2.51, 4.1.2.14, 4.1.2.21
UniProt: Q6KZI8
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	2-dehydro-3-deoxy-D-GLUCONATE/2-dehydro-3-deoxy- phosphogluconate aldolase (EC 4.1.2.51, 4.1.2.14, 4.1.2.21)	protein	274	45% helix, 14% strand	Q6KZI8

Ligands and binding sites

GOL · Glycerol · additive · 19 copies · chains A, B, D, C
EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D
IPA · Isopropyl alcohol · additive · 3 copies · chains A, B, D
PEG · Di(hydroxyethyl)ether · additive · chains B, C
PGE · Triethylene glycol · additive · chains 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	73	0.74	0.98	25	empty
2	71	0.73	0.98	25	empty
3	351	0.64	0.79	47	GOL, IPA
4	335	0.64	0.79	44	GOL, EDO, PGE
5	321	0.64	0.79	39	GOL, EDO

Interfaces

4 interfaces between chains.

A–B · 1695 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1676 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 766 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 709 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4UXD · 2-keto 3-deoxygluconate aldolase from Picrophilus torridus · the same entry in another collection · chain A against A, TM-score 1.00
Q6KZI8 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxy-D… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q6KZI8
Elsewhere: RCSB PDB 4UXD · PDBe 4UXD · UniProt Q6KZI8

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