MolNFT v1 · #68583 · protein + RNA

Crystal structure of the E. COLI thim riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module

3K0J · U1 small nuclear ribonucleoprotein a: “Crystal structure of the E. COLI thim riboswitch in complex with thiamine pyrophosphate and the U1A…”. X-ray diffraction, 2 ligands (TPP, MG), 10 pockets (best druggability 0.81). MolNFT v1…

PDB: 3K0J
Type: protein + RNA
Length: 526 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U1 small nuclear ribonucleoprotein a; RNA (87-mer)
UniProt: P09012
Ligands: TPP, MG
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	U1 small nuclear ribonucleoprotein a	protein	92	36% helix, 28% strand	P09012
C	U1 small nuclear ribonucleoprotein a	protein	86	27% helix, 23% strand	P09012
D	U1 small nuclear ribonucleoprotein a	protein	82	29% helix, 29% strand	P09012
E, F	RNA (87-mer)	rna	87	—	—

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 2 copies · chains E, F
MG · Magnesium ion · metal · 8 copies · chains E, F

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.81	0.84	76	TPP, MG
2	754	0.79	0.84	68	TPP, MG
3	70	0.71	0.96	32	empty
4	211	0.53	0.77	30	empty
5	210	0.43	0.73	14	empty

Interfaces

10 interfaces between chains.

B–F · 1220 Å² buried · 32 hydrogen bonds · protein-nucleic
A–E · 1173 Å² buried · 33 hydrogen bonds · protein-nucleic
A–D · 466 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 431 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 429 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3K0J · Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate… · the same entry in another collection · chain A against A, TM-score 1.00

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 3K0J · PDBe 3K0J · UniProt P09012

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