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2-deoxyribose-5-phosphate aldolase from lactobacillus brevis

Analyse 2-deoxyribose-5-phosphate aldolase from lactobacillus brevis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XBK
Type: protein
Length: 434 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: U2PI02
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Deoxyribose-phosphate aldolase (EC 4.1.2.4)	protein	217	49% helix, 16% strand	U2PI02

Ligands and binding sites

ACY · Acetic acid · additive · 3 copies · chains 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	115	0.46	0.79	24	empty
2	134	0.46	0.77	23	empty
3	112	0.45	0.78	24	ACY

Interfaces

1 interface between chains.

A–B · 1485 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4XBK · 2-deoxyribose-5-phosphate aldolase from Lactobacillus brevis · 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 U2PI02
Elsewhere: RCSB PDB 4XBK · PDBe 4XBK · UniProt U2PI02

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