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Structure of sprlmcd with U747 RNA
Analyse Structure of sprlmcd with U747 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XJ2
- Type
- protein + RNA
- Length
- 1,819 residues
- Chains
- 5
- 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, ZN
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 5 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 | 454 | 27% helix, 31% strand | Q97R12 |
| B | Uncharacterized RNA methyltransferase SP_1029 (EC 2.1.1.-) | protein | 452 | 25% helix, 32% strand | Q97R12 |
| C | Uncharacterized RNA methyltransferase SP_1029 (EC 2.1.1.-) | protein | 451 | 27% helix, 31% strand | Q97R12 |
| D | Uncharacterized RNA methyltransferase SP_1029 (EC 2.1.1.-) | protein | 452 | 26% helix, 33% strand | Q97R12 |
| G | RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3') | rna | 10 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.74 | 0.77 | 97 | ZN, SAH |
| 2 | 591 | 0.73 | 0.80 | 57 | empty |
| 3 | 768 | 0.72 | 0.78 | 78 | SAH |
| 4 | 735 | 0.71 | 0.77 | 82 | ZN, SAH |
| 5 | 714 | 0.70 | 0.77 | 72 | SAH |
Interfaces
4 interfaces between chains.
- A–G · 535 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 499 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 366 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 5XJ2 · PDBe 5XJ2 · UniProt Q97R12
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