MolNFT v1 · #85035 · RNA
X-ray crystal structures of 70S ribosome functional complexes
486D · P-site tRNA of 70S ribosome: “X-ray crystal structures of 70S ribosome functional complexes”. X-ray diffraction, 1 ligand (IR), 8 pockets (best druggability 0.69). MolNFT v1 #85035 on GenesisL1: 3D structure, binding sites and…
- PDB
- 486D
- Type
- RNA
- Length
- 224 nucleotides
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-site tRNA of 70S ribosome; P-site codon of 70S ribosome; A-site tRNA of 70S ribosome…
- Ligands
- IR
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P-site tRNA of 70S ribosome | rna | 74 | — | — |
| B | P-site codon of 70S ribosome | rna | 3 | — | — |
| C | A-site tRNA of 70S ribosome | rna | 72 | — | — |
| D | A-site codon of 70S ribosome | rna | 3 | — | — |
| E | E-site tRNA of 70S ribosome | rna | 72 | — | — |
Ligands and binding sites
- IR · Iridium ion · metal · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.69 | 0.75 | 37 | empty |
| 2 | 646 | 0.65 | 0.76 | 32 | empty |
| 3 | 667 | 0.62 | 0.74 | 30 | empty |
| 4 | 311 | 0.54 | 0.76 | 22 | empty |
| 5 | 345 | 0.53 | 0.75 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 174 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- A–B · 170 Ų buried · 12 hydrogen bonds · nucleic-nucleic
- A–C · 137 Ų buried · 10 hydrogen bonds · nucleic-nucleic
- B–D · 45 Ų buried · 1 hydrogen bond · nucleic-nucleic
- A–E · 31 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 29 modified (nucleotide modification).
Compared structures
- 486D · X-ray crystal structures of 70S ribosome functional complexes · 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
- Elsewhere: RCSB PDB 486D · PDBe 486D
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