Research workbench

Arginase from medicago truncatula

Analyse Arginase from medicago truncatula in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VSS
Type: protein
Length: 1,905 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginase
EC: 3.5.3.1
UniProt: G7JFU5
Ligands: MN
Pockets: 17 · best druggability 0.88

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arginase (EC 3.5.3.1)	protein	316	46% helix, 18% strand	G7JFU5
B	Arginase (EC 3.5.3.1)	protein	319	45% helix, 18% strand	G7JFU5
C, D, F	Arginase (EC 3.5.3.1)	protein	318	45% helix, 18% strand	G7JFU5
E	Arginase (EC 3.5.3.1)	protein	316	45% helix, 18% strand	G7JFU5

Ligands and binding sites

MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F

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

Pockets

17 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	836	0.88	0.91	112	empty
2	367	0.82	0.91	48	empty
3	821	0.80	0.83	80	empty
4	808	0.79	0.82	77	empty
5	527	0.73	0.82	58	empty

Interfaces

12 interfaces between chains.

B–E · 1756 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 1717 Å² buried · 21 hydrogen bonds · protein-protein
C–F · 1686 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 924 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 897 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6VSS · Arginase from Medicago truncatula · the same entry in another collection · chain F against F, TM-score 1.00
G7JFU5 · AlphaFold monomer V2.0 prediction for arginase, mitochondrial (G7JFU5) · a predicted model of the same protein · chain D 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 G7JFU5
Elsewhere: RCSB PDB 6VSS · PDBe 6VSS · UniProt G7JFU5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.