MolNFT v1 · #179406 · protein

Human arginase 1 in complex with compound 51.

7K4J · Arginase-1: “Human arginase 1 in complex with compound 51.”. X-ray diffraction, 2 ligands (VV1, MN), 20 pockets (best druggability 0.79). MolNFT v1 #179406 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K4J
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: VV1, MN
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 43% 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	43% helix, 16% strand	P05089

Ligands and binding sites

VV1 · 3-[(1~{S},2~{S},5~{R})-2-carboxy-3,6-diazabicyclo[3.2.0]heptan-1-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	774	0.79	0.82	68	empty
2	1161	0.77	0.79	93	empty
3	561	0.65	0.76	60	empty
4	296	0.56	0.76	30	empty
5	205	0.54	0.78	32	empty

Interfaces

8 interfaces between chains.

C–F · 999 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 996 Å² buried · 22 hydrogen bonds · protein-protein
A–E · 991 Å² buried · 24 hydrogen bonds · protein-protein
B–E · 983 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 977 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

7K4J · Human Arginase 1 in complex with compound 51. · 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 7K4J · PDBe 7K4J · UniProt P05089

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