MolNFT v1 · #25006 · protein

Crystal structure of degs after backsoaking the activating peptide

1VCW · Protease degs: “Crystal structure of degs after backsoaking the activating peptide”. X-ray diffraction, 8 pockets (best druggability 0.70). MolNFT v1 #25006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VCW
Type: protein
Length: 873 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease degs
EC: 3.4.21.-
UniProt: P31137
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Protease degs (EC 3.4.21.-)	protein	291	14% helix, 35% strand	P31137

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	403	0.70	0.82	52	empty
2	134	0.69	0.89	37	empty
3	61	0.68	0.97	18	empty
4	131	0.68	0.89	36	empty
5	119	0.66	0.89	37	empty

Interfaces

3 interfaces between chains.

B–C · 1099 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1065 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1064 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1VCW · Crystal structure of DegS after backsoaking the activating peptide · 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 P31137
Elsewhere: RCSB PDB 1VCW · PDBe 1VCW · UniProt P31137

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