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Crystal structure of porcine RNase 4 D80A mutant in complex with dcmp

Analyse Crystal structure of porcine RNase 4 D80A mutant in complex with dcmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ARL
Type: protein
Length: 482 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: DCM
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribonuclease 4 (EC 3.1.27.-)	protein	121	26% helix, 33% strand	P15468
C, D	Ribonuclease 4 (EC 3.1.27.-)	protein	120	26% helix, 34% strand	P15468

Ligands and binding sites

DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

5 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	338	0.57	0.76	29	empty
2	174	0.49	0.77	29	DCM
3	105	0.44	0.79	22	empty
4	85	0.41	0.79	21	empty
5	54	0.28	0.74	14	DCM

Interfaces

4 interfaces between chains.

B–D · 327 Å² buried · 1 hydrogen bond · protein-protein
A–C · 327 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 163 Å² buried · 1 hydrogen bond · protein-protein
B–C · 34 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5ARL · crystal structure of porcine RNase 4 D80A mutant in complex with dCMP · 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 0.97

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 5ARL · PDBe 5ARL · UniProt P15468

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