MolNFT v1 · #18726 · protein

Crystal structure of ribonuclease SA2

1PY3: “Crystal structure of ribonuclease SA2”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.64). MolNFT v1 #18726 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PY3
Type: protein
Length: 279 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease
EC: 3.1.4.8
UniProt: Q53752
Ligands: SO4
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease (EC 3.1.4.8)	protein	94	16% helix, 23% strand	Q53752
B	Ribonuclease (EC 3.1.4.8)	protein	93	16% helix, 23% strand	Q53752
C	Ribonuclease (EC 3.1.4.8)	protein	92	15% helix, 26% strand	Q53752

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A, C

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

Pockets

2 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	182	0.64	0.85	37	empty
2	104	0.40	0.76	28	empty

Interfaces

2 interfaces between chains.

B–C · 848 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 595 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1PY3 · Crystal structure of Ribonuclease Sa2 · the same entry in another collection · 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 Q53752
Elsewhere: RCSB PDB 1PY3 · PDBe 1PY3 · UniProt Q53752

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.