MolNFT v1 · #116443 · protein + RNA
L-glutamine riboswitch bound with L-glutamine soaked with cs+
5DDR · L-glutamine riboswitch RNA (61-mer): “L-glutamine riboswitch bound with L-glutamine soaked with cs+”. X-ray diffraction, 5 ligands (GLN, MG, K), 6 pockets (best druggability 0.70). MolNFT v1 #116443 on GenesisL1: 3D structure…
- PDB
- 5DDR
- Type
- protein + RNA
- Length
- 310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-glutamine riboswitch RNA (61-mer); U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- GLN, MG, K, CS, NA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-glutamine riboswitch RNA (61-mer) | rna | 61 | — | — |
| C | U1 small nuclear ribonucleoprotein a | protein | 94 | 28% helix, 21% strand | P09012 |
| D | U1 small nuclear ribonucleoprotein a | protein | 94 | 30% helix, 24% strand | P09012 |
Ligands and binding sites
- GLN · Glutamine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 11 copies · chains A, B, C
- K · Potassium ion · metal · 7 copies · chains A, B
- CS · Cesium ion · metal · 7 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.70 | 0.80 | 33 | K, MG, CS |
| 2 | 613 | 0.69 | 0.79 | 31 | K, MG |
| 3 | 689 | 0.68 | 0.77 | 44 | GLN, MG |
| 4 | 376 | 0.54 | 0.74 | 20 | K, MG, CS |
| 5 | 341 | 0.52 | 0.74 | 18 | MG, CS |
Interfaces
4 interfaces between chains.
- A–D · 1015 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 1001 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–B · 459 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- B–D · 128 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5DDR · L-glutamine riboswitch bound with L-glutamine soaked with Cs+ · 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 5DDR · PDBe 5DDR · UniProt P09012
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