MolNFT v1 · #179404 · protein

Human arginase 1 in complex with compound 04.

7K4H · Arginase-1: “Human arginase 1 in complex with compound 04.”. X-ray diffraction, 2 ligands (VV4, MN), 20 pockets (best druggability 0.78). MolNFT v1 #179404 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K4H
Type: protein
Length: 1,908 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: VV4, MN
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 41% 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	318	41% helix, 16% strand	P05089

Ligands and binding sites

VV4 · 3-[(1~{R},5~{S},8~{R})-5-carboxy-2,6-diazabicyclo[3.2.1]octan-8-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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	923	0.78	0.81	73	empty
2	823	0.78	0.81	66	empty
3	603	0.66	0.76	66	empty
4	355	0.58	0.76	41	empty
5	318	0.57	0.76	31	empty

Interfaces

8 interfaces between chains.

C–E · 1026 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1020 Å² buried · 23 hydrogen bonds · protein-protein
A–F · 1014 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1007 Å² buried · 22 hydrogen bonds · protein-protein
B–F · 1003 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

7K4H · Human Arginase 1 in complex with compound 04. · 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 7K4H · PDBe 7K4H · UniProt P05089

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