MolNFT v1 · #155539 · protein + RNA
The wildtype SAM-VI riboswitch bound to sah
6LAU · RNA (54-mer): “The wildtype SAM-VI riboswitch bound to sah”. X-ray diffraction, 3 ligands (SAH, GTP, CS), 8 pockets (best druggability 0.71). MolNFT v1 #155539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LAU
- Type
- protein + RNA
- Length
- 379 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (54-mer); U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- SAH, GTP, CS
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (54-mer) | rna | 54 | — | — |
| B | RNA (54-mer) | rna | 55 | — | — |
| C | U1 small nuclear ribonucleoprotein a | protein | 91 | 34% helix, 25% strand | P09012 |
| E | U1 small nuclear ribonucleoprotein a | protein | 92 | 32% helix, 25% strand | P09012 |
| D | U1 small nuclear ribonucleoprotein a | protein | 87 | 37% helix, 29% strand | P09012 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- CS · Cesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.71 | 0.79 | 59 | empty |
| 2 | 551 | 0.70 | 0.80 | 36 | CS |
| 3 | 565 | 0.69 | 0.79 | 46 | empty |
| 4 | 119 | 0.53 | 0.82 | 19 | empty |
| 5 | 55 | 0.32 | 0.78 | 11 | SAH |
Interfaces
6 interfaces between chains.
- A–E · 1214 Ų buried · 40 hydrogen bonds · protein-nucleic
- B–C · 1155 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–D · 671 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–D · 423 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 10 modified, 1 covalent (engineered, covalent ligand).
Compared structures
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 6LAU · PDBe 6LAU · UniProt P09012
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