MolNFT v1 · #72075 · protein + RNA
Native structure of a C-di-gmp riboswitch from V. cholerae
3MXH · U1 small nuclear ribonucleoprotein a: “Native structure of a C-di-gmp riboswitch from V. cholerae”. X-ray diffraction, 2 ligands (C2E, MG), 4 pockets (best druggability 0.68). MolNFT v1 #72075 on GenesisL1: 3D structure, binding…
- PDB
- 3MXH
- Type
- protein + RNA
- Length
- 179 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
- C2E, MG
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | U1 small nuclear ribonucleoprotein a | protein | 87 | 25% helix, 26% strand | P09012 |
| R | C-di-gmp riboswitch | rna | 92 | — | — |
Ligands and binding sites
- 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 · 5 copies · chains P, 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.68 | 0.77 | 48 | empty |
| 2 | 506 | 0.63 | 0.77 | 30 | MG |
| 3 | 396 | 0.58 | 0.76 | 24 | MG |
| 4 | 86 | 0.38 | 0.78 | 11 | C2E |
Interfaces
1 interface between chains.
- P–R · 1015 Ų buried · 24 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3MXH · Native structure of a c-di-GMP riboswitch from V. cholerae · the same entry in another collection · chain R against R, 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 0.97
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 P09012
- Elsewhere: RCSB PDB 3MXH · PDBe 3MXH · UniProt P09012
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