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Crystal structure of feii hppe in complex with substrate form 2
Analyse Crystal structure of feii hppe in complex with substrate form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZZ8
- Type
- protein
- Length
- 577 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxypropylphosphonic acid epoxidase
- EC
- 1.14.-.-
- UniProt
- Q56185
- Ligands
- S0H, FE2
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxypropylphosphonic acid epoxidase (EC 1.14.-.-) | protein | 192 | 24% helix, 31% strand | Q56185 |
| B | Hydroxypropylphosphonic acid epoxidase (EC 1.14.-.-) | protein | 193 | 25% helix, 30% strand | Q56185 |
| C | Hydroxypropylphosphonic acid epoxidase (EC 1.14.-.-) | protein | 192 | 24% helix, 30% strand | Q56185 |
Ligands and binding sites
- S0H · (S)-2-hydroxypropylphosphonic acid · ligand · 3 copies · chains A, B, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.63 | 0.77 | 38 | empty |
| 2 | 269 | 0.60 | 0.79 | 37 | FE2, S0H |
| 3 | 229 | 0.59 | 0.80 | 33 | FE2, S0H |
| 4 | 78 | 0.48 | 0.82 | 15 | FE2, S0H |
| 5 | 145 | 0.42 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1530 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 150 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1ZZ8 · Crystal Structure of FeII HppE in Complex with Substrate Form 2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q56185 · AlphaFold monomer V2.0 prediction for (S)-2-hydroxypropylphosphonic acid epoxidase… · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q56185
- Elsewhere: RCSB PDB 1ZZ8 · PDBe 1ZZ8 · UniProt Q56185
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