MolNFT v1 · #115998 · protein + RNA
Crystal structure of epoxyqueuosine reductase with cleaved RNA stem loop
5D0A: “Crystal structure of epoxyqueuosine reductase with cleaved RNA stem loop”. X-ray diffraction, 3 ligands (SF4, B12, PO4), 20 pockets (best druggability 0.84). MolNFT v1 #115998 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5D0A
- Type
- protein + RNA
- Length
- 1,533 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxyqueuosine reductase; RNA (5'- R(*G*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'…
- EC
- 1.17.99.6
- UniProt
- P97030
- Ligands
- SF4, B12, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 379 | 47% helix, 12% strand | P97030 |
| C | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 376 | 47% helix, 12% strand | P97030 |
| D | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 375 | 47% helix, 12% strand | P97030 |
| E | RNA (5'- R(*G*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') | rna | 11 | — | — |
| F | RNA (5'- R(*G*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') | rna | 13 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, C, D
- B12 · Cobalamin · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.84 | 0.85 | 64 | SF4, B12, GOL |
| 2 | 1024 | 0.84 | 0.84 | 65 | SF4, B12, GOL |
| 3 | 1011 | 0.83 | 0.84 | 66 | SF4, B12, GOL |
| 4 | 1027 | 0.83 | 0.84 | 66 | SF4, B12, GOL |
| 5 | 522 | 0.66 | 0.78 | 41 | empty |
Interfaces
7 interfaces between chains.
- A–C · 931 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 900 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 328 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 305 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–E · 276 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5D0A · Crystal structure of epoxyqueuosine reductase with cleaved RNA stem loop · the same entry in another collection · chain F against F, TM-score 1.00
- P97030 · AlphaFold monomer V2.0 prediction for epoxyqueuosine reductase (P97030) · a predicted model of the same protein · chain D 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 P97030
- Elsewhere: RCSB PDB 5D0A · PDBe 5D0A · UniProt P97030
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