MolNFT v1 · #113843 · protein

Crystal structure of porcine RNase 4 D80A mutant

5ARJ · Ribonuclease 4: “Crystal structure of porcine RNase 4 D80A mutant”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #113843 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ARJ
Type: protein
Length: 481 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease 4
EC: 3.1.27.-
UniProt: P15468
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease 4 (EC 3.1.27.-)	protein	120	26% helix, 34% strand	P15468
B	Ribonuclease 4 (EC 3.1.27.-)	protein	119	24% helix, 34% strand	P15468
C, D	Ribonuclease 4 (EC 3.1.27.-)	protein	121	26% helix, 34% strand	P15468

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	679	0.67	0.76	73	empty
2	120	0.44	0.78	21	empty
3	88	0.41	0.79	22	empty
4	54	0.25	0.73	15	empty

Interfaces

4 interfaces between chains.

B–C · 392 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 332 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 191 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 37 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5ARJ · crystal structure of porcine RNase 4 D80A mutant · the same entry in another collection · chain A against A, TM-score 1.00
P15468 · AlphaFold monomer V2.0 prediction for ribonuclease 4 (P15468) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P15468
Elsewhere: RCSB PDB 5ARJ · PDBe 5ARJ · UniProt P15468

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