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Optimization of the in silico designed kemp eliminase KE70 by computational design and directed evolution R2 3/5G

Analyse Optimization of the in silico designed kemp eliminase KE70 by computational… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NQ2
Type: protein
Length: 491 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyribose phosphate aldolase
Pockets: 1 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyribose phosphate aldolase	protein	247	49% helix, 15% strand	—
B	Deoxyribose phosphate aldolase	protein	244	50% helix, 16% strand	—

Ligands and binding sites

IMD · Imidazole · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1183	0.79	0.80	109	IMD

Interfaces

1 interface between chains.

A–B · 282 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3NQ2 · Optimization of the in silico designed Kemp eliminase KE70 by computational design and… · 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
Elsewhere: RCSB PDB 3NQ2 · PDBe 3NQ2

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