Research workbench
Crystal structure of alkyl hydroperoxidase D (ahpd) from streptococcus pneumoniae (strain D39/ nctc 7466)
Analyse Crystal structure of alkyl hydroperoxidase D (ahpd) from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E8L
- Type
- protein
- Length
- 1,087 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyl hydroperoxide reductase ahpd
- EC
- 1.11.1.15
- UniProt
- A0A0H2ZNM1
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Alkyl hydroperoxide reductase ahpd (EC 1.11.1.15) | protein | 180 | 68% helix, 0% strand | A0A0H2ZNM1 |
| B, C, F | Alkyl hydroperoxide reductase ahpd (EC 1.11.1.15) | protein | 182 | 68% helix, 0% strand | A0A0H2ZNM1 |
| E | Alkyl hydroperoxide reductase ahpd (EC 1.11.1.15) | protein | 181 | 69% helix, 0% strand | A0A0H2ZNM1 |
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 | 690 | 0.79 | 0.83 | 71 | empty |
| 2 | 356 | 0.75 | 0.86 | 36 | empty |
| 3 | 346 | 0.74 | 0.85 | 32 | empty |
| 4 | 418 | 0.73 | 0.83 | 31 | empty |
| 5 | 362 | 0.73 | 0.84 | 35 | empty |
Interfaces
8 interfaces between chains.
- C–E · 2077 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 2067 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2052 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 422 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 392 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6E8L · Crystal Structure of Alkyl hydroperoxidase D (AhpD) from Streptococcus pneumoniae (Strain… · 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 A0A0H2ZNM1
- Elsewhere: RCSB PDB 6E8L · PDBe 6E8L · UniProt A0A0H2ZNM1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.