MolNFT v1 · #113844 · protein

Crystal structure of porcine RNase 4 in complex with dump

5ARK · Ribonuclease 4: “Crystal structure of porcine RNase 4 in complex with dump”. X-ray diffraction, 2 ligands (UMP, PO4), 5 pockets (best druggability 0.72). MolNFT v1 #113844 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5ARK
Type: protein
Length: 476 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease 4
EC: 3.1.27.-
UniProt: P15468
Ligands: UMP, PO4
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ribonuclease 4 (EC 3.1.27.-)	protein	119	25% helix, 35% strand	P15468

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 2 copies · chains A, C, B

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

Pockets

5 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	637	0.72	0.79	61	UMP
2	408	0.69	0.81	52	UMP
3	659	0.65	0.75	41	PO4
4	56	0.29	0.75	17	empty
5	52	0.24	0.72	14	UMP

Interfaces

6 interfaces between chains.

B–C · 787 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 499 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 377 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 148 Å² buried · 1 hydrogen bond · protein-protein
A–B · 29 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5ARK · crystal structure of porcine RNase 4 in complex with dUMP · 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 A against A, TM-score 0.98

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 5ARK · PDBe 5ARK · UniProt P15468

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