Research workbench
Crystal structure of sprlmcd with U747 stemloop RNA
Analyse Crystal structure of sprlmcd with U747 stemloop RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZQ8
- Type
- protein + RNA
- Length
- 932 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized RNA methyltransferase SP_1029; RNA…
- EC
- 2.1.1.-
- UniProt
- Q97R12
- Ligands
- SAH, NI
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Uncharacterized RNA methyltransferase SP_1029 (EC 2.1.1.-) | protein | 454 | 25% helix, 33% strand | Q97R12 |
| C, D | RNA (5'-R(*CP*CP*GP*UP*(MUM)P*GP*AP*AP*AP*AP*GP*G)-3') | rna | 12 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains B, C, A, D
- NI · Nickel (II) ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.77 | 0.81 | 65 | SAH, NI |
| 2 | 689 | 0.71 | 0.78 | 66 | SAH |
| 3 | 474 | 0.69 | 0.80 | 49 | NI |
| 4 | 181 | 0.51 | 0.77 | 30 | empty |
| 5 | 72 | 0.35 | 0.76 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1236 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–D · 1231 Ų buried · 39 hydrogen bonds · protein-nucleic
- C–D · 192 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- B–A · 30 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 15 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ZQ8 · Crystal structure of spRlmCD with U747 stemloop RNA · the same entry in another collection · chain B against B, TM-score 1.00
- Q97R12 · AlphaFold monomer V2.0 prediction for uncharacterized RNA methyltransferase SP_1029… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q97R12
- Elsewhere: RCSB PDB 5ZQ8 · PDBe 5ZQ8 · UniProt Q97R12
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