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Arginase from bacillus caldevelox, L-ornithine complex

Analyse Arginase from bacillus caldevelox, L-ornithine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CEV
Type: protein
Length: 1,788 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: ORN, GAI, MN
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Protein (arginase) (EC 3.5.3.1)	protein	298	43% helix, 17% strand	P53608

Ligands and binding sites

ORN · L-ornithine · ligand · 6 copies · chains A, B, C, D, E, F
GAI · Guanidine · ligand · 6 copies · chains A, B, C, D, E, F
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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	879	0.77	0.80	61	empty
2	883	0.77	0.80	63	empty
3	182	0.56	0.80	20	GAI
4	150	0.55	0.81	18	GAI
5	132	0.55	0.82	23	GAI

Interfaces

7 interfaces between chains.

A–C · 686 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 662 Å² buried · 12 hydrogen bonds · protein-protein
D–F · 660 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 660 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 660 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4CEV · Arginase from bacillus caldevelox, L-ornithine complex · the same entry in another collection · chain F against F, TM-score 1.00
P53608 · AlphaFold monomer V2.0 prediction for arginase (P53608) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 4CEV · PDBe 4CEV · UniProt P53608

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