MolNFT v1 · #122455 · protein

Structure of bacillus nanornase a active site mutant bound to a mononucleotide

5IPP · Bifunctional oligoribonuclease and pap phosphatase nrna: “Structure of bacillus nanornase a active site mutant bound to a mononucleotide”. X-ray diffraction, 1 ligand (AMP), 8 pockets (best druggability 0.72). MolNFT v1 #122455 on…

PDB: 5IPP
Type: protein
Length: 1,261 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional oligoribonuclease and pap phosphatase nrna
EC: 3.1.3.7
UniProt: O34600
Ligands: AMP
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bifunctional oligoribonuclease and pap phosphatase nrna (EC 3.1.3.7)	protein	315	45% helix, 19% strand	O34600
B, D	Bifunctional oligoribonuclease and pap phosphatase nrna (EC 3.1.3.7)	protein	316	46% helix, 19% strand	O34600
C	Bifunctional oligoribonuclease and pap phosphatase nrna (EC 3.1.3.7)	protein	314	46% helix, 19% strand	O34600

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	841	0.72	0.77	58	empty
2	802	0.70	0.76	58	empty
3	271	0.49	0.74	35	empty
4	222	0.48	0.75	35	empty
5	117	0.47	0.79	20	empty

Interfaces

3 interfaces between chains.

B–C · 1691 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1675 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 972 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5IPP · Structure of Bacillus NanoRNase A active site mutant bound to a mononucleotide · the same entry in another collection · chain D against D, TM-score 1.00
O34600 · AlphaFold monomer V2.0 prediction for bifunctional oligoribonuclease and pap phosphatase… · 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 O34600
Elsewhere: RCSB PDB 5IPP · PDBe 5IPP · UniProt O34600

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