Research workbench

Arginase-dehydro-abh complex

Analyse Arginase-dehydro-abh complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1T4P
Type: protein
Length: 942 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginase 1
EC: 3.5.3.1
UniProt: P07824
Ligands: 2BH, MN
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Arginase 1 (EC 3.5.3.1)	protein	314	41% helix, 16% strand	P07824

Ligands and binding sites

2BH · [(1E,5S)-5-amino-5-carboxypent-1-enyl](trihydroxy)borate(1-) · ligand · 3 copies · chains A, B, C
MN · Manganese (II) ion · metal · 6 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	805	0.81	0.84	63	empty
2	331	0.56	0.75	33	empty
3	121	0.52	0.81	21	empty
4	139	0.52	0.80	27	empty
5	121	0.49	0.80	24	2BH

Interfaces

3 interfaces between chains.

A–C · 988 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 976 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 973 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1T4P · Arginase-dehydro-ABH complex · the same entry in another collection · chain A against A, TM-score 1.00
P07824 · AlphaFold monomer V2.0 prediction for arginase-1 (P07824) · 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 P07824
Elsewhere: RCSB PDB 1T4P · PDBe 1T4P · UniProt P07824

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