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Human ARGINASE1 complexed with bicyclic inhibitor compound 13

Analyse Human ARGINASE1 complexed with bicyclic inhibitor compound 13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V7F
Type: protein
Length: 1,911 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: QRJ, MN
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Arginase-1 (EC 3.5.3.1)	protein	318	42% helix, 16% strand	P05089
B, E, F	Arginase-1 (EC 3.5.3.1)	protein	319	41% helix, 16% strand	P05089

Ligands and binding sites

QRJ · {3-[(5R,7S,8S)-8-azaniumyl-8-carboxy-2-azaspiro[4.4]nonan-2-ium-7-yl]propyl}(trihydroxy) borate(1-) · 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	730	0.79	0.83	59	empty
2	1196	0.77	0.79	107	empty
3	200	0.54	0.78	29	empty
4	275	0.54	0.76	31	empty
5	263	0.54	0.76	32	empty

Interfaces

8 interfaces between chains.

B–E · 1012 Å² buried · 21 hydrogen bonds · protein-protein
A–E · 1012 Å² buried · 23 hydrogen bonds · protein-protein
D–F · 1011 Å² buried · 24 hydrogen bonds · protein-protein
C–F · 998 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 987 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6V7F · Human Arginase1 Complexed with Bicyclic Inhibitor Compound 13 · 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 C 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 6V7F · PDBe 6V7F · UniProt P05089

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