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Crystal structure of a catalytically inactive cxc chemokine-degrading protease spycep from streptococcus pyogenes

Analyse Crystal structure of a catalytically inactive cxc chemokine-degrading protease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VJB
Type: protein
Length: 1,346 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative cell envelope proteinase
UniProt: Q9A180
Ligands: CA
Pockets: 19 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative cell envelope proteinase	protein	1346	12% helix, 37% strand	Q9A180

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.77	0.98	24	empty
2	877	0.75	0.79	82	empty
3	1107	0.73	0.76	76	empty
4	291	0.70	0.84	34	empty
5	390	0.65	0.78	39	empty

Compared structures

6VJB · Crystal structure of a catalytically inactive CXC Chemokine-degrading protease SpyCEP… · 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
Every structure of UniProt Q9A180
Elsewhere: RCSB PDB 6VJB · PDBe 6VJB · UniProt Q9A180

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