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Catalytically active tobacco etch virus protease complexed with product

Analyse Catalytically active tobacco etch virus protease complexed with product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LVM
Type: protein
Length: 467 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalytic domain of the nuclear inclusion protein a (nia); Oligopeptide substrate for the…
UniProt: P04517
Ligands: ACE
Pockets: 4 · best druggability 0.37

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Catalytic domain of the nuclear inclusion protein a (nia)	protein	229	10% helix, 41% strand	P04517
B	Catalytic domain of the nuclear inclusion protein a (nia)	protein	219	11% helix, 43% strand	P04517
C, D	Oligopeptide substrate for the protease	protein	6	0% helix, 50% strand	P04517
E	Catalytic domain of the nuclear inclusion protein a (nia)	protein	7	0% helix, 29% strand	P04517

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	78	0.37	0.77	13	empty
2	79	0.36	0.76	16	empty
3	104	0.36	0.74	26	empty
4	60	0.31	0.75	16	empty

Interfaces

4 interfaces between chains.

A–B · 1654 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 725 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 725 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 436 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1LVM · Catalytically active tobacco etch virus protease complexed with product · 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 P04517
Elsewhere: RCSB PDB 1LVM · PDBe 1LVM · UniProt P04517

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