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Human arginase 1 in complex with compound 52.

Analyse Human arginase 1 in complex with compound 52. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K4K
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: VUS, MN
Pockets: 20 · best druggability 0.78

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Arginase-1 (EC 3.5.3.1)	protein	317	42% helix, 16% strand	P05089

Ligands and binding sites

VUS · 3-[(3~{A}~{S},4~{S},6~{A}~{R})-4-carboxy-2,3,4,5,6, 6~{A}-hexahydro-1~{H}-pyrrolo[2,3-c]pyrrol-3~{A}-yl]propyl-$L^{3}-oxidanyl-bis(oxidanyl)boranuide · 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	935	0.78	0.80	74	empty
2	1142	0.78	0.80	97	empty
3	570	0.66	0.76	60	empty
4	349	0.57	0.76	41	empty
5	316	0.56	0.76	32	empty

Interfaces

8 interfaces between chains.

A–E · 991 Å² buried · 24 hydrogen bonds · protein-protein
B–E · 979 Å² buried · 22 hydrogen bonds · protein-protein
C–F · 976 Å² buried · 20 hydrogen bonds · protein-protein
D–F · 967 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 967 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

7K4K · Human Arginase 1 in complex with compound 52. · 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 7K4K · PDBe 7K4K · UniProt P05089

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