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Evolutionary optimization of computationally designed enzymes: kemp eliminases of the KE07 series

Analyse Evolutionary optimization of computationally designed enzymes: kemp eliminases… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IIO
Type: protein
Length: 1,492 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KE07
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, F	KE07	protein	248	40% helix, 25% strand	—
B, D	KE07	protein	250	39% helix, 24% strand	—

Pockets

11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1094	0.80	0.81	110	empty
2	1135	0.78	0.80	84	empty
3	909	0.77	0.80	79	empty
4	330	0.66	0.81	48	empty
5	667	0.66	0.75	63	empty

Interfaces

5 interfaces between chains.

A–C · 759 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 565 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 479 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 418 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 55 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3IIO · Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the… · 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 3IIO · PDBe 3IIO

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