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Crystal structure of gentlyase, the neutral metalloprotease of paenibacillus polymyxa

Analyse Crystal structure of gentlyase, the neutral metalloprotease of paenibacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GER
Type: protein
Length: 612 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gentlyase metalloprotease
EC: 3.4.24.4
Ligands: CA, ZN
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Gentlyase metalloprotease (EC 3.4.24.4)	protein	306	43% helix, 18% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

3 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	589	0.77	0.84	60	empty
2	78	0.42	0.80	22	empty
3	67	0.40	0.80	26	empty

Interfaces

1 interface between chains.

A–B · 860 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4GER · Crystal structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa · 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 4GER · PDBe 4GER

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