Research workbench

Arginase-dinor-noha complex

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

PDB: 1T4T
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: DIR, MN
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Arginase 1 (EC 3.5.3.1)	protein	314	41% helix, 17% strand	P07824

Ligands and binding sites

DIR · 3-{[(E)-amino(hydroxyimino)methyl]amino}alanine · 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

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	763	0.81	0.84	64	empty
2	341	0.58	0.76	35	empty
3	118	0.52	0.81	22	empty
4	100	0.45	0.80	23	DIR
5	80	0.44	0.81	19	DIR

Interfaces

3 interfaces between chains.

B–C · 958 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 949 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 925 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1T4T · arginase-dinor-NOHA 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 1T4T · PDBe 1T4T · UniProt P07824

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