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Crystal structure of the de novo designed protein 200 AA in the crystal form 2

Analyse Crystal structure of the de novo designed protein 200 AA in the crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8YL8
Type: protein
Length: 820 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.21
Source: Escherichia coli
Molecule: De novo protein
Ligands: SO4
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · resolution 2.21 · 2 distinct chains · 66% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	De novo protein	protein	211	65% helix, 10% strand	—
C, D	De novo protein	protein	199	66% helix, 11% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	560	0.63	0.75	65	SO4
2	343	0.57	0.76	33	empty
3	102	0.42	0.77	15	SO4
4	100	0.39	0.76	18	empty
5	85	0.38	0.76	14	SO4

Interfaces

4 interfaces between chains.

A–B · 291 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 267 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 262 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 16 Å² buried · 0 hydrogen bonds · protein-protein

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8YL8 · PDBe 8YL8

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