MolNFT v1 · #116440 · protein + RNA
Structural and dynamic basis for low affinity-high selectivity binding of L-glutamine by the gln-riboswitch
5DDO · L-glutamine riboswitch (58-mer): “Structural and dynamic basis for low affinity-high selectivity binding of L-glutamine by the gln-riboswitch”. X-ray diffraction, 7 pockets (best druggability 0.72). MolNFT v1 #116440 on GenesisL1…
- PDB
- 5DDO
- Type
- protein + RNA
- Length
- 289 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-glutamine riboswitch (58-mer); U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-glutamine riboswitch (58-mer) | rna | 58 | — | — |
| G | U1 small nuclear ribonucleoprotein a | protein | 86 | 29% helix, 29% strand | P09012 |
| C | U1 small nuclear ribonucleoprotein a | protein | 87 | 33% helix, 22% strand | P09012 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.72 | 0.77 | 49 | empty |
| 2 | 376 | 0.52 | 0.73 | 26 | empty |
| 3 | 238 | 0.45 | 0.73 | 16 | empty |
| 4 | 81 | 0.40 | 0.78 | 17 | empty |
| 5 | 93 | 0.38 | 0.77 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–G · 904 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 834 Ų buried · 24 hydrogen bonds · protein-nucleic
- G–C · 292 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 96 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 5DDO · Structural and Dynamic Basis for Low Affinity-High Selectivity Binding of L-glutamine by… · 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 5DDO · PDBe 5DDO · UniProt P09012
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