MolNFT v1 · #62203 · protein

X-ray structure of rat arginase I-T135A: the unliganded complex

3E8Q · Arginase-1: “X-ray structure of rat arginase I-T135A: the unliganded complex”. X-ray diffraction, 1 ligand (MN), 8 pockets (best druggability 0.81). MolNFT v1 #62203 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3E8Q
Type: protein
Length: 924 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginase-1
EC: 3.5.3.1
UniProt: P07824
Ligands: MN
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Arginase-1 (EC 3.5.3.1)	protein	308	40% helix, 16% strand	P07824

Ligands and binding sites

MN · Manganese (II) ion · metal · 6 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	754	0.81	0.85	51	empty
2	345	0.57	0.75	41	empty
3	301	0.56	0.76	32	empty
4	188	0.54	0.79	28	empty
5	135	0.52	0.81	29	empty

Interfaces

3 interfaces between chains.

A–C · 762 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 755 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 740 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3E8Q · X-ray structure of rat arginase I-T135A: the unliganded complex · the same entry in another collection · chain B against B, TM-score 1.00
P07824 · AlphaFold monomer V2.0 prediction for arginase-1 (P07824) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P07824
Elsewhere: RCSB PDB 3E8Q · PDBe 3E8Q · UniProt P07824

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