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Arginase from bacillus caldovelox, native structure at pH 5.6

Analyse Arginase from bacillus caldovelox, native structure at pH 5.6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CEV
Type: protein
Length: 1,794 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (arginase)
EC: 3.5.3.1
UniProt: P53608
Ligands: MN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Protein (arginase) (EC 3.5.3.1)	protein	299	42% helix, 18% strand	P53608

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

20 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	931	0.85	0.86	91	empty
2	710	0.79	0.84	67	empty
3	678	0.79	0.84	59	empty
4	303	0.64	0.80	37	empty
5	256	0.55	0.77	38	empty

Interfaces

10 interfaces between chains.

A–C · 657 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 652 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 647 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 643 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 635 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1CEV · Arginase from bacillus caldovelox, native structure at pH 5.6 · the same entry in another collection · chain C against C, TM-score 1.00
P53608 · AlphaFold monomer V2.0 prediction for arginase (P53608) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P53608
Elsewhere: RCSB PDB 1CEV · PDBe 1CEV · UniProt P53608

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