Research workbench
L-glutamine riboswitch bound with L-glutamine soaked with MN2+
Analyse L-glutamine riboswitch bound with L-glutamine soaked with MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DDQ
- Type
- protein + RNA
- Length
- 309 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, NA, MN, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% 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 | 33% helix, 26% strand | P09012 |
| D | U1 small nuclear ribonucleoprotein a | protein | 93 | 28% helix, 26% strand | P09012 |
Ligands and binding sites
- GLN · Glutamine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 5 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.77 | 0.80 | 63 | NA, GLN, MN |
| 2 | 606 | 0.74 | 0.81 | 43 | NA |
| 3 | 324 | 0.50 | 0.74 | 20 | NA |
| 4 | 291 | 0.48 | 0.73 | 19 | MG |
| 5 | 79 | 0.28 | 0.72 | 12 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1090 Ų buried · 39 hydrogen bonds · protein-nucleic
- A–D · 1015 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–B · 479 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- B–D · 143 Ų buried · 1 hydrogen bond · protein-nucleic
- A–C · 11 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5DDQ · L-glutamine riboswitch bound with L-glutamine soaked with Mn2+ · 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 5DDQ · PDBe 5DDQ · UniProt P09012
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