MolNFT v1 · #116441 · protein + RNA
L-glutamine riboswitch bound with L-glutamine
5DDP · RNA (61-mer): “L-glutamine riboswitch bound with L-glutamine”. X-ray diffraction, 3 ligands (GLN, NA, MG), 7 pockets (best druggability 0.72). MolNFT v1 #116441 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DDP
- Type
- protein + RNA
- Length
- 309 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (61-mer); U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- GLN, NA, MG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (61-mer) | rna | 61 | — | — |
| C | U1 small nuclear ribonucleoprotein a | protein | 93 | 28% helix, 25% strand | P09012 |
| D | U1 small nuclear ribonucleoprotein a | protein | 94 | 32% helix, 26% strand | P09012 |
Ligands and binding sites
- GLN · Glutamine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 10 copies · chains A, B
- MG · Magnesium ion · metal · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.72 | 0.81 | 38 | NA |
| 2 | 553 | 0.69 | 0.79 | 32 | NA |
| 3 | 715 | 0.68 | 0.77 | 46 | GLN, MG |
| 4 | 333 | 0.51 | 0.74 | 18 | MG, NA |
| 5 | 311 | 0.49 | 0.73 | 20 | MG, NA |
Interfaces
4 interfaces between chains.
- B–C · 1048 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–D · 1000 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–B · 465 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- B–D · 98 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5DDP · L-glutamine riboswitch bound with L-glutamine · 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 5DDP · PDBe 5DDP · UniProt P09012
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