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Lysozyme 056 from deep neural language modeling

Analyse Lysozyme 056 from deep neural language modeling in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RGR
Type: protein
Length: 333 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Artificial protein L056
EC: 3.2.1.17
Ligands: CL
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 60% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Artificial protein L056 (EC 3.2.1.17)	protein	167	59% helix, 10% strand	—
A	Artificial protein L056 (EC 3.2.1.17)	protein	166	61% helix, 10% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains B, A
NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains B, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	280	0.60	0.79	21	empty
2	112	0.40	0.75	16	empty
3	78	0.37	0.77	19	empty
4	110	0.34	0.72	15	empty
5	56	0.24	0.71	15	empty

Interfaces

1 interface between chains.

B–A · 931 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

7RGR · Lysozyme 056 from Deep neural language modeling · the same entry in another collection · chain B against B, 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 7RGR · PDBe 7RGR

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