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Human ARGINASE1 complexed with inhibitor compound 24A

Analyse Human ARGINASE1 complexed with inhibitor compound 24A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KLM
Type: protein
Length: 1,902 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginase-1
EC: 3.5.3.1
UniProt: P05089
Ligands: 0IZ, MN
Pockets: 20 · best druggability 0.78

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Arginase-1 (EC 3.5.3.1)	protein	317	41% helix, 17% strand	P05089

Ligands and binding sites

0IZ · 3-[(2~{S},3~{R},4~{R})-4-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]-2-carboxy-pyrrolidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boron · 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	917	0.78	0.81	67	empty
2	941	0.78	0.80	74	empty
3	574	0.65	0.76	60	empty
4	279	0.56	0.76	32	empty
5	261	0.55	0.77	31	empty

Interfaces

8 interfaces between chains.

D–F · 989 Å² buried · 23 hydrogen bonds · protein-protein
B–E · 988 Å² buried · 23 hydrogen bonds · protein-protein
C–F · 985 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 982 Å² buried · 22 hydrogen bonds · protein-protein
A–E · 981 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

7KLM · Human Arginase1 Complexed with Inhibitor Compound 24a · the same entry in another collection · chain F against F, 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 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 P05089
Elsewhere: RCSB PDB 7KLM · PDBe 7KLM · UniProt P05089

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