MolNFT v1 · #177046 · protein
Crystal structure of PHM7
7E5U · Diels-alderase: “Crystal structure of PHM7”. X-ray diffraction, 2 ligands (SO4, CL), 9 pockets (best druggability 0.91). MolNFT v1 #177046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E5U
- Type
- protein
- Length
- 1,121 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diels-alderase
- UniProt
- A0A2Z5XAU0
- Ligands
- SO4, CL
- Pockets
- 9 · best druggability 0.91
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diels-alderase | protein | 373 | 5% helix, 55% strand | A0A2Z5XAU0 |
| C | Diels-alderase | protein | 375 | 5% helix, 55% strand | A0A2Z5XAU0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 19 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.91 | 0.94 | 143 | GOL, SO4 |
| 2 | 246 | 0.83 | 0.94 | 32 | GOL, SO4 |
| 3 | 187 | 0.62 | 0.83 | 41 | empty |
| 4 | 538 | 0.58 | 0.73 | 61 | GOL, SO4 |
| 5 | 193 | 0.54 | 0.79 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–C · 876 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 759 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 688 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7E5U · Crystal structure of Phm7 · 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 7E5U · PDBe 7E5U · UniProt A0A2Z5XAU0
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