MolNFT v1 · #155537 · protein + RNA
The wildtype SAM-VI riboswitch bound to SAM
6LAS · RNA (55-mer): “The wildtype SAM-VI riboswitch bound to SAM”. X-ray diffraction, 1 ligand (SAM), 9 pockets (best druggability 0.69). MolNFT v1 #155537 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LAS
- Type
- protein + RNA
- Length
- 381 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (55-mer); U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- SAM
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (55-mer) | rna | 55 | — | — |
| C | U1 small nuclear ribonucleoprotein a | protein | 91 | 29% helix, 26% strand | P09012 |
| E | U1 small nuclear ribonucleoprotein a | protein | 93 | 34% helix, 25% strand | P09012 |
| D | U1 small nuclear ribonucleoprotein a | protein | 87 | 36% helix, 26% strand | P09012 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.69 | 0.79 | 58 | empty |
| 2 | 634 | 0.68 | 0.78 | 38 | empty |
| 3 | 503 | 0.67 | 0.79 | 28 | empty |
| 4 | 113 | 0.49 | 0.81 | 16 | empty |
| 5 | 218 | 0.45 | 0.74 | 18 | SAM |
Interfaces
6 interfaces between chains.
- A–E · 1202 Ų buried · 42 hydrogen bonds · protein-nucleic
- B–C · 1156 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–D · 672 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 450 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 98 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 6LAS · the wildtype SAM-VI riboswitch bound to SAM · 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 6LAS · PDBe 6LAS · UniProt P09012
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