MolNFT v1 · #93106 · protein

Crystal structure of NI2+2-human arginase I

4GSM · Arginase-1: “Crystal structure of NI2+2-human arginase I”. X-ray diffraction, 1 ligand (NI), 4 pockets (best druggability 0.73). MolNFT v1 #93106 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GSM
Type: protein
Length: 626 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginase-1
EC: 3.5.3.1
UniProt: P05089
Ligands: NI
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Arginase-1 (EC 3.5.3.1)	protein	313	42% helix, 17% strand	P05089

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.73	0.76	93	empty
2	85	0.42	0.80	21	empty
3	53	0.40	0.81	14	empty
4	58	0.35	0.78	14	empty

Interfaces

1 interface between chains.

A–B · 259 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4GSM · Crystal Structure of Ni2+2-Human Arginase I · the same entry in another collection · chain A against A, 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 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 P05089
Elsewhere: RCSB PDB 4GSM · PDBe 4GSM · UniProt P05089

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