MolNFT v1 · #142111 · protein + RNA
Crystal structure of sprlmcd with U1939LOOP RNA at 3.24 ångström
5ZTH · Uncharacterized RNA methyltransferase SP_1029: “Crystal structure of sprlmcd with U1939LOOP RNA at 3.24 ångström”. X-ray diffraction, 1 ligand (SAH), 2 pockets (best druggability 0.74). MolNFT v1 #142111 on GenesisL1: 3D structure…
- PDB
- 5ZTH
- Type
- protein + RNA
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized RNA methyltransferase SP_1029; RNA (5'-R(P*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3')
- EC
- 2.1.1.-
- UniProt
- Q97R12
- Ligands
- SAH
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized RNA methyltransferase SP_1029 (EC 2.1.1.-) | protein | 453 | 26% helix, 32% strand | Q97R12 |
| B | RNA (5'-R(P*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3') | rna | 8 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.74 | 0.80 | 83 | SAH |
| 2 | 74 | 0.35 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1082 Ų buried · 35 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5ZTH · Crystal structure of spRlmCD with U1939loop RNA at 3.24 angstrom · 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 5ZTH · PDBe 5ZTH · UniProt Q97R12
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