Research workbench
Crystal structure of era in complex with mggdpnp, nucleotides 1506- 1542 of 16S ribosomal RNA, and ksga
Analyse Crystal structure of era in complex with mggdpnp, nucleotides 1506- 1542 of 16S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R9X
- Type
- protein + RNA
- Length
- 572 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase era; Ribosomal RNA small subunit methyltransferase a; RNA301
- EC
- 2.1.1.182
- UniProt
- O67800, O67680
- Ligands
- GNP, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase era | protein | 302 | 40% helix, 24% strand | O67800 |
| B | Ribosomal RNA small subunit methyltransferase a (EC 2.1.1.182) | protein | 235 | 42% helix, 18% strand | O67680 |
| C | RNA301 | rna | 35 | — | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.69 | 0.79 | 64 | MG, GNP |
| 2 | 466 | 0.69 | 0.80 | 44 | empty |
| 3 | 174 | 0.48 | 0.76 | 22 | empty |
| 4 | 70 | 0.46 | 0.82 | 20 | empty |
| 5 | 61 | 0.32 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1541 Ų buried · 44 hydrogen bonds · protein-nucleic
- B–C · 413 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3R9X · Crystal structure of Era in complex with MgGDPNP, nucleotides 1506-1542 of 16S ribosomal… · the same entry in another collection · chain A against A, TM-score 1.00
- O67800 · AlphaFold monomer V2.0 prediction for GTPase era (O67800) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O67680 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase a… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O67800
- Every structure of UniProt O67680
- Elsewhere: RCSB PDB 3R9X · PDBe 3R9X · UniProt O67800 · UniProt O67680
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