MolNFT v1 · #171566 · protein

Escherichia COLI D-2-deoxyribose-5-phosphate aldolase - N21K mutant

6Z9J · Deoxyribose-phosphate aldolase: “Escherichia COLI D-2-deoxyribose-5-phosphate aldolase - N21K mutant”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.77). MolNFT v1 #171566 on GenesisL1: 3D structure, binding sites…

PDB: 6Z9J
Type: protein
Length: 499 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyribose-phosphate aldolase
EC: 4.1.2.4
UniProt: E2QLE1
Ligands: MG
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyribose-phosphate aldolase (EC 4.1.2.4)	protein	250	50% helix, 15% strand	E2QLE1
B	Deoxyribose-phosphate aldolase (EC 4.1.2.4)	protein	249	49% helix, 15% strand	E2QLE1

Ligands and binding sites

MG · Magnesium ion · metal · 9 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	523	0.77	0.84	53	MG
2	120	0.52	0.82	22	empty
3	107	0.50	0.82	23	empty

Interfaces

1 interface between chains.

A–B · 673 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6Z9J · Escherichia coli D-2-deoxyribose-5-phosphate aldolase - N21K mutant · the same entry in another collection · chain A against A, TM-score 1.00

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 E2QLE1
Elsewhere: RCSB PDB 6Z9J · PDBe 6Z9J · UniProt E2QLE1

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