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The X-ray crystal structure of the paramecium bursaria chlorella virus arginine decarboxylase bound to agmatine

Analyse The X-ray crystal structure of the paramecium bursaria chlorella virus arginine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NVA
Type: protein
Length: 2,946 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginine decarboxylase, A207R protein
EC: 4.1.1.19
UniProt: Q84527
Ligands: PL2
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arginine decarboxylase, A207R protein (EC 4.1.1.19)	protein	369	36% helix, 25% strand	Q84527
B	Arginine decarboxylase, A207R protein (EC 4.1.1.19)	protein	369	35% helix, 25% strand	Q84527
C	Arginine decarboxylase, A207R protein (EC 4.1.1.19)	protein	367	36% helix, 25% strand	Q84527
D	Arginine decarboxylase, A207R protein (EC 4.1.1.19)	protein	371	35% helix, 25% strand	Q84527
E	Arginine decarboxylase, A207R protein (EC 4.1.1.19)	protein	370	35% helix, 25% strand	Q84527
F	Arginine decarboxylase, A207R protein (EC 4.1.1.19)	protein	368	36% helix, 25% strand	Q84527
G	Arginine decarboxylase, A207R protein (EC 4.1.1.19)	protein	368	35% helix, 26% strand	Q84527
H	Arginine decarboxylase, A207R protein (EC 4.1.1.19)	protein	364	35% helix, 25% strand	Q84527

Ligands and binding sites

PL2 · (4-{[(4-{[amino(imino)methyl]amino}butyl)amino]methyl}-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.81	0.83	134	PL2
2	1196	0.81	0.82	106	empty
3	108	0.77	0.97	35	PL2
4	104	0.77	0.97	31	PL2
5	805	0.77	0.81	106	empty

Interfaces

16 interfaces between chains.

C–D · 2582 Å² buried · 36 hydrogen bonds · protein-protein
G–H · 2569 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 2555 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 2539 Å² buried · 37 hydrogen bonds · protein-protein
B–D · 787 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2NVA · The X-ray crystal structure of the Paramecium bursaria Chlorella virus arginine… · the same entry in another collection · chain C against C, 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 Q84527
Elsewhere: RCSB PDB 2NVA · PDBe 2NVA · UniProt Q84527

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