MolNFT v1 · #155544 · protein + RNA
The wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1
6LAZ · RNA (55-mer): “The wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1”. X-ray diffraction, 2 ligands (E7X, MG), 9 pockets (best druggability 0.69). MolNFT v1 #155544 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6LAZ
- 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
- E7X, MG
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (55-mer) | rna | 55 | — | — |
| C, E | U1 small nuclear ribonucleoprotein a | protein | 91 | 26% helix, 25% strand | P09012 |
| D | U1 small nuclear ribonucleoprotein a | protein | 89 | 34% helix, 26% strand | P09012 |
Ligands and binding sites
- E7X · (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.69 | 0.80 | 27 | empty |
| 2 | 495 | 0.69 | 0.80 | 34 | MG |
| 3 | 518 | 0.68 | 0.79 | 60 | empty |
| 4 | 107 | 0.56 | 0.85 | 22 | empty |
| 5 | 206 | 0.43 | 0.74 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–E · 1225 Ų buried · 40 hydrogen bonds · protein-nucleic
- B–C · 1184 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–D · 559 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 401 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 89 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6LAZ · the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 · 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 6LAZ · PDBe 6LAZ · UniProt P09012
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.