Research workbench
Structure of MOEN5-SSO7D fusion protein in complex with a permethylated substrate analogue
Analyse Structure of MOEN5-SSO7D fusion protein in complex with a permethylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GWW
- Type
- protein
- Length
- 1,191 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MOEN5,DNA-binding protein 7D
- UniProt
- A0A010, P39476
- Ligands
- 7B5
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MOEN5,DNA-binding protein 7D | protein | 264 | 78% helix, 0% strand | A0A010, P39476 |
| B | MOEN5,DNA-binding protein 7D | protein | 332 | 67% helix, 10% strand | A0A010, P39476 |
| C | MOEN5,DNA-binding protein 7D | protein | 262 | 78% helix, 0% strand | A0A010, P39476 |
| D | MOEN5,DNA-binding protein 7D | protein | 333 | 65% helix, 9% strand | A0A010, P39476 |
Ligands and binding sites
- 7B5 · methyl (2R)-3-dimethoxyphosphoryloxy-2-[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoate · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.82 | 0.83 | 80 | empty |
| 2 | 1120 | 0.79 | 0.80 | 75 | empty |
| 3 | 698 | 0.78 | 0.83 | 65 | empty |
| 4 | 648 | 0.75 | 0.81 | 45 | 7B5 |
| 5 | 297 | 0.57 | 0.77 | 50 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1854 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1844 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 828 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 323 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5GWW · Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue · the same entry in another collection · chain D against D, TM-score 1.00
- P39476 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P39476) · a predicted model of the same protein · chain D against A, TM-score 0.19
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 A0A010
- Every structure of UniProt P39476
- Elsewhere: RCSB PDB 5GWW · PDBe 5GWW · UniProt A0A010 · UniProt P39476
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