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Optimization of the in silico designed kemp eliminase KE70 by computational design and directed evolution

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: 3Q2D
Type: protein
Length: 473 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyribose phosphate aldolase
Ligands: 3NY
Pockets: 4 · best druggability 0.71

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyribose phosphate aldolase	protein	246	50% helix, 16% strand	—
B	Deoxyribose phosphate aldolase	protein	227	51% helix, 14% strand	—

Ligands and binding sites

3NY · 5-nitro-1H-benzotriazole · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	532	0.71	0.80	62	3NY
2	219	0.63	0.83	45	3NY
3	187	0.59	0.82	24	empty
4	211	0.59	0.81	23	empty

Interfaces

1 interface between chains.

A–B · 586 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3Q2D · 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 3Q2D · PDBe 3Q2D

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