Research workbench
Crystal structure of PHM7 in complex with inhibitor
Analyse Crystal structure of PHM7 in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E5V
- Type
- protein
- Length
- 1,116 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diels-alderase
- UniProt
- A0A2Z5XAU0
- Ligands
- HZC, SO4
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diels-alderase | protein | 372 | 5% helix, 55% strand | A0A2Z5XAU0 |
| C | Diels-alderase | protein | 372 | 5% helix, 53% strand | A0A2Z5XAU0 |
Ligands and binding sites
- HZC · [(1S,2S,5R)-5-methyl-2-propan-2-yl-cyclohexyl]methanamine · ligand · 7 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 13 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.86 | 0.93 | 53 | GOL |
| 2 | 266 | 0.84 | 0.95 | 32 | HZC |
| 3 | 224 | 0.81 | 0.94 | 30 | HZC |
| 4 | 563 | 0.80 | 0.86 | 55 | GOL |
| 5 | 144 | 0.76 | 0.94 | 28 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 967 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 724 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 673 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7E5V · Crystal structure of Phm7 in complex with inhibitor · 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 A0A2Z5XAU0
- Elsewhere: RCSB PDB 7E5V · PDBe 7E5V · UniProt A0A2Z5XAU0
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