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Crystal structure of arginase from bacillus subtilis

Analyse Crystal structure of arginase from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DKT
Type: protein
Length: 1,680 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginase
EC: 3.5.3.1
UniProt: P39138
Ligands: MN
Pockets: 19 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Arginase (EC 3.5.3.1)	protein	283	45% helix, 17% strand	P39138
E	Arginase (EC 3.5.3.1)	protein	268	44% helix, 20% strand	P39138
F	Arginase (EC 3.5.3.1)	protein	280	44% helix, 19% strand	P39138

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

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1024	0.80	0.82	88	empty
2	1076	0.78	0.80	74	empty
3	721	0.74	0.80	69	empty
4	482	0.62	0.76	50	empty
5	232	0.57	0.79	25	empty

Interfaces

10 interfaces between chains.

A–B · 681 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 668 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 652 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 652 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 389 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6DKT · Crystal structure of Arginase from Bacillus subtilis · the same entry in another collection · chain F against F, TM-score 1.00
P39138 · AlphaFold monomer V2.0 prediction for arginase (P39138) · a predicted model of the same protein · chain C 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 P39138
Elsewhere: RCSB PDB 6DKT · PDBe 6DKT · UniProt P39138

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