MolNFT v1 · #142253 · protein
Crystal structure of domain-swapped circular-permuted ybea (CP74) from escherichia COLI
5ZYO · Ribosomal RNA large subunit methyltransferase H: “Crystal structure of domain-swapped circular-permuted ybea (CP74) from escherichia COLI”. X-ray diffraction, 9 pockets (best druggability 0.62). MolNFT v1 #142253 on GenesisL1: 3D…
- PDB
- 5ZYO
- Type
- protein
- Length
- 598 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase H
- EC
- 2.1.1.177
- UniProt
- P0A8I8
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase H (EC 2.1.1.177) | protein | 154 | 42% helix, 19% strand | P0A8I8 |
| B | Ribosomal RNA large subunit methyltransferase H (EC 2.1.1.177) | protein | 140 | 46% helix, 19% strand | P0A8I8 |
| C, D | Ribosomal RNA large subunit methyltransferase H (EC 2.1.1.177) | protein | 152 | 46% helix, 18% strand | P0A8I8 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.62 | 0.78 | 57 | empty |
| 2 | 280 | 0.59 | 0.78 | 45 | empty |
| 3 | 193 | 0.59 | 0.81 | 21 | empty |
| 4 | 115 | 0.47 | 0.80 | 25 | empty |
| 5 | 144 | 0.45 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4860 Ų buried · 76 hydrogen bonds · protein-protein
- B–D · 4697 Ų buried · 70 hydrogen bonds · protein-protein
- A–D · 304 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 268 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 258 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ZYO · Crystal Structure of domain-swapped Circular-Permuted YbeA (CP74) from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P0A8I8 · AlphaFold monomer V2.0 prediction for ribosomal RNA large subunit methyltransferase H… · a predicted model of the same protein · chain B against A, TM-score 0.43
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 P0A8I8
- Elsewhere: RCSB PDB 5ZYO · PDBe 5ZYO · UniProt P0A8I8
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