MolNFT v1 · #67688 · protein + RNA

Structure of a C-di-gmp riboswitch from V. cholerae

3IRW · U1 small nuclear ribonucleoprotein a: “Structure of a C-di-gmp riboswitch from V. cholerae”. X-ray diffraction, 3 ligands (IRI, C2E, MG), 4 pockets (best druggability 0.69). MolNFT v1 #67688 on GenesisL1: 3D structure, binding sites…

PDB: 3IRW
Type: protein + RNA
Length: 181 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U1 small nuclear ribonucleoprotein a; C-di-gmp riboswitch
UniProt: P09012
Ligands: IRI, C2E, MG
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	U1 small nuclear ribonucleoprotein a	protein	90	30% helix, 27% strand	P09012
R	C-di-gmp riboswitch	rna	91	—	—

Ligands and binding sites

IRI · Iridium hexammine ion · ligand · 9 copies · chains R
C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · chains R
MG · Magnesium ion · metal · 2 copies · chains R

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

Pockets

4 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	684	0.69	0.77	46	IRI
2	555	0.66	0.78	32	IRI
3	422	0.57	0.76	30	IRI
4	81	0.37	0.78	10	C2E

Interfaces

1 interface between chains.

P–R · 976 Å² buried · 27 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

3IRW · Structure of a c-di-GMP riboswitch from V. cholerae · the same entry in another collection · chain P against P, TM-score 1.00
P09012 · AlphaFold monomer V2.0 prediction for U1 small nuclear ribonucleoprotein a (P09012) · a predicted model of the same protein · chain P 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 P09012
Elsewhere: RCSB PDB 3IRW · PDBe 3IRW · UniProt P09012

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