Research workbench
Crystal structure of a putative RNA methyltransferase PH1948 from pyrococcus horikoshii
Analyse Crystal structure of a putative RNA methyltransferase PH1948 from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WY7
- Type
- protein
- Length
- 799 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH1948
- EC
- 2.1.1.-
- UniProt
- O59611
- Ligands
- SAH
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein PH1948 (EC 2.1.1.-) | protein | 196 | 36% helix, 27% strand | O59611 |
| B | Hypothetical protein PH1948 (EC 2.1.1.-) | protein | 198 | 37% helix, 27% strand | O59611 |
| C | Hypothetical protein PH1948 (EC 2.1.1.-) | protein | 201 | 36% helix, 26% strand | O59611 |
| D | Hypothetical protein PH1948 (EC 2.1.1.-) | protein | 204 | 36% helix, 25% strand | O59611 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.69 | 0.89 | 30 | SAH |
| 2 | 183 | 0.67 | 0.86 | 33 | SAH |
| 3 | 155 | 0.67 | 0.87 | 33 | SAH |
| 4 | 155 | 0.66 | 0.87 | 31 | SAH |
| 5 | 260 | 0.60 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–D · 486 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 274 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1WY7 · crystal structure of a putative RNA methyltransferase PH1948 from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
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 O59611
- Elsewhere: RCSB PDB 1WY7 · PDBe 1WY7 · UniProt O59611
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