MolNFT v1 · #62224 · protein

X-ray structure of rat arginase I-T135A mutant: the complex with bec

3E9B · Arginase-1: “X-ray structure of rat arginase I-T135A mutant: the complex with bec”. X-ray diffraction, 2 ligands (S2C, MN), 9 pockets (best druggability 0.81). MolNFT v1 #62224 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3E9B
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: S2C, MN
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Arginase-1 (EC 3.5.3.1)	protein	308	41% helix, 15% strand	P07824

Ligands and binding sites

S2C · S-2-(boronoethyl)-L-cysteine · ligand · 3 copies · chains A, B, C
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

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.81	0.82	90	empty
2	232	0.58	0.80	30	empty
3	329	0.56	0.75	34	empty
4	99	0.47	0.81	23	S2C
5	108	0.46	0.80	23	S2C

Interfaces

3 interfaces between chains.

A–C · 754 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 742 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 736 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3E9B · X-ray structure of rat arginase I-T135A mutant: the complex with BEC · the same entry in another collection · chain C against C, TM-score 1.00
P07824 · AlphaFold monomer V2.0 prediction for arginase-1 (P07824) · a predicted model of the same protein · chain B 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 3E9B · PDBe 3E9B · UniProt P07824

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