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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: 3IIV
Type: protein
Length: 510 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KE7 KE7_R7_1/3H
Ligands: MG
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	KE7 KE7_R7_1/3H	protein	248	41% helix, 25% strand	—
B	KE7 KE7_R7_1/3H	protein	262	37% helix, 24% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · chains B

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

Pockets

5 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	343	0.67	0.81	47	empty
2	333	0.62	0.79	49	MG
3	283	0.51	0.74	32	empty
4	121	0.49	0.79	18	empty
5	61	0.26	0.72	13	empty

Interfaces

1 interface between chains.

A–B · 464 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3IIV · Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3IIV · PDBe 3IIV

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