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Crystal structure of alkylhydroperoxidase ahpd core: uncharacterized peroxidase-related protein (YP_296737.1) from ralstonia eutropha JMP134 at 2.15 a resolution
Analyse Crystal structure of alkylhydroperoxidase ahpd core: uncharacterized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PRR
- Type
- protein
- Length
- 2,276 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkylhydroperoxidase ahpd core: uncharacterized peroxidase- related protein
- UniProt
- Q46Y90
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, H | Alkylhydroperoxidase ahpd core: uncharacterized peroxidase- related protein | protein | 190 | 71% helix, 0% strand | Q46Y90 |
| C, G, I, L | Alkylhydroperoxidase ahpd core: uncharacterized peroxidase- related protein | protein | 189 | 70% helix, 0% strand | Q46Y90 |
| D, K | Alkylhydroperoxidase ahpd core: uncharacterized peroxidase- related protein | protein | 191 | 71% helix, 0% strand | Q46Y90 |
| J | Alkylhydroperoxidase ahpd core: uncharacterized peroxidase- related protein | protein | 188 | 72% helix, 0% strand | Q46Y90 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 25 copies · chains A, B, D, E, H, I, C, G, K, L, F, J
- PGE · Triethylene glycol · additive · 7 copies · chains B, I, C, K, A, D, E, H, F, L, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.72 | 0.84 | 50 | PGE |
| 2 | 317 | 0.71 | 0.84 | 49 | PGE |
| 3 | 341 | 0.70 | 0.83 | 51 | PGE |
| 4 | 363 | 0.70 | 0.83 | 57 | PGE |
| 5 | 350 | 0.70 | 0.83 | 51 | PGE |
Interfaces
25 interfaces between chains.
- C–G · 2005 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 1989 Ų buried · 40 hydrogen bonds · protein-protein
- H–I · 1986 Ų buried · 41 hydrogen bonds · protein-protein
- K–L · 1975 Ų buried · 40 hydrogen bonds · protein-protein
- F–J · 1975 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 2PRR · Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related… · 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 Q46Y90
- Elsewhere: RCSB PDB 2PRR · PDBe 2PRR · UniProt Q46Y90
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