MolNFT v1 · #18742 · protein

Crystal structure of ribonuclease SA2

1PYL: “Crystal structure of ribonuclease SA2”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.51). MolNFT v1 #18742 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PYL
Type: protein
Length: 190 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease
EC: 3.1.4.8
UniProt: Q53752
Ligands: SO4
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease (EC 3.1.4.8)	protein	96	16% helix, 23% strand	Q53752
B	Ribonuclease (EC 3.1.4.8)	protein	94	15% helix, 23% strand	Q53752

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B

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

Pockets

3 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	80	0.51	0.84	17	empty
2	71	0.36	0.77	21	SO4
3	59	0.32	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 547 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1PYL · 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 1PYL · PDBe 1PYL · UniProt Q53752

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