Research workbench
crystal structure of yeast Coq5 in the SAM bound form
Analyse crystal structure of yeast Coq5 in the SAM bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OBW
- Type
- protein
- Length
- 936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Saccharomyces cerevisiae
- Molecule
- 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
- EC
- 2.1.1.201
- UniProt
- P49017
- Ligands
- SAM, TAM
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (EC 2.1.1.201) | protein | 234 | 48% helix, 21% strand | P49017 |
| D, C | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (EC 2.1.1.201) | protein | 235 | 48% helix, 21% strand | P49017 |
| B | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (EC 2.1.1.201) | protein | 232 | 48% helix, 22% strand | P49017 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, D, C, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.71 | 0.76 | 75 | empty |
| 2 | 221 | 0.69 | 0.86 | 38 | SAM |
| 3 | 197 | 0.68 | 0.87 | 32 | SAM |
| 4 | 292 | 0.66 | 0.82 | 45 | SAM |
| 5 | 254 | 0.66 | 0.83 | 37 | SAM |
Interfaces
6 interfaces between chains.
- A–B · 1094 Ų buried · 0 hydrogen bonds · protein-protein
- D–C · 1070 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 4 hydrogen bonds · protein-protein
- D–B · 257 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OBW · Crystal structure of yeast COQ5 in the SAM bound form · the same entry in another collection · chain D against D, TM-score 1.00
- P49017 · AlphaFold monomer V2.0 prediction for 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase… · a predicted model of the same protein · chain B 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 P49017
- Elsewhere: RCSB PDB 4OBW · PDBe 4OBW · UniProt P49017
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