Research workbench

X-ray structure of human arginase I: the mutant D183A in complex with abh

Analyse X-ray structure of human arginase I: the mutant D183A in complex with abh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3E6K
Type: protein
Length: 616 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: ABH, MN
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Arginase-1 (EC 3.5.3.1)	protein	308	42% helix, 16% strand	P05089

Ligands and binding sites

ABH · 2(S)-amino-6-boronohexanoic acid · 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

5 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	991	0.72	0.76	84	ABH
2	64	0.42	0.81	14	empty
3	99	0.41	0.78	20	ABH
4	75	0.38	0.77	16	empty
5	68	0.30	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 290 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3E6K · X-ray structure of Human Arginase I: the mutant D183A in complex with ABH · 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 A 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 3E6K · PDBe 3E6K · UniProt P05089

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