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Crystal structure of human arginase-1 complexed with inhibitor 14

Analyse Crystal structure of human arginase-1 complexed with inhibitor 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HXQ
Type: protein
Length: 628 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginase-1
EC: 3.5.3.1
UniProt: P05089
Ligands: X8A, MN
Pockets: 4 · best druggability 0.78

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Arginase-1 (EC 3.5.3.1)	protein	314	43% helix, 17% strand	P05089

Ligands and binding sites

X8A · [(5R)-5-carboxy-5-(methylamino)-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-) · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	935	0.78	0.81	87	X8A
2	96	0.43	0.79	19	X8A
3	51	0.35	0.79	14	empty
4	50	0.32	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 495 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4HXQ · Crystal structure of human Arginase-1 complexed with inhibitor 14 · the same entry in another collection · chain A against A, TM-score 1.00
P05089 · AlphaFold monomer V2.0 prediction for arginase-1 (P05089) · a predicted model of the same protein · chain B 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 P05089
Elsewhere: RCSB PDB 4HXQ · PDBe 4HXQ · UniProt P05089

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