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Crystal structure of the E. COLI thim riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module
Analyse Crystal structure of the E. COLI thim riboswitch in complex with thiamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–E · 1173 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–D · 466 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 431 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 429 Ų 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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