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Crystal structure of alkylhydroperoxidase ahpd core (YP_425393.1) from rhodospirillum rubrum atcc 11170 at 1.95 a resolution
Analyse Crystal structure of alkylhydroperoxidase ahpd core (YP_425393.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OUW
- Type
- protein
- Length
- 271 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkylhydroperoxidase ahpd core
- EC
- 1.-.-.-
- UniProt
- Q2RXN9
- Ligands
- UNL, NA
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkylhydroperoxidase ahpd core (EC 1.-.-.-) | protein | 135 | 70% helix, 0% strand | Q2RXN9 |
| B | Alkylhydroperoxidase ahpd core (EC 1.-.-.-) | protein | 136 | 69% helix, 0% strand | Q2RXN9 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- ACY · Acetic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.64 | 0.83 | 26 | UNL |
| 2 | 201 | 0.63 | 0.82 | 26 | UNL, ACY |
Interfaces
1 interface between chains.
- A–B · 2891 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 2OUW · Crystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum… · 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 Q2RXN9
- Elsewhere: RCSB PDB 2OUW · PDBe 2OUW · UniProt Q2RXN9
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