Research workbench
Crystal structure of reduced chimeric E.COLI AHPC1-186-yfskhn
Analyse Crystal structure of reduced chimeric E.COLI AHPC1-186-yfskhn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B8B
- Type
- protein
- Length
- 1,649 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2
- EC
- 1.11.1.15
- UniProt
- P0AE08, P32119
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 165 | 33% helix, 28% strand | P0AE08, P32119 |
| B, I | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 163 | 34% helix, 28% strand | P0AE08, P32119 |
| J, C, E | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 166 | 34% helix, 28% strand | P0AE08, P32119 |
| D | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 164 | 34% helix, 28% strand | P0AE08, P32119 |
| F, H | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 167 | 34% helix, 28% strand | P0AE08, P32119 |
| G | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 162 | 35% helix, 30% strand | P0AE08, P32119 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, C, D, E, F, G, I, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.75 | 0.94 | 21 | empty |
| 2 | 134 | 0.75 | 0.93 | 22 | empty |
| 3 | 106 | 0.74 | 0.95 | 21 | empty |
| 4 | 114 | 0.72 | 0.93 | 18 | empty |
| 5 | 126 | 0.72 | 0.92 | 21 | empty |
Interfaces
10 interfaces between chains.
- F–E · 1246 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1237 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1226 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1193 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1077 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5B8B · Crystal structure of reduced chimeric E.coli AhpC1-186-YFSKHN · the same entry in another collection · chain J against J, TM-score 1.00
- P0AE08 · AlphaFold monomer V2.0 prediction for alkyl hydroperoxide reductase C (P0AE08) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P0AE08
- Every structure of UniProt P32119
- Elsewhere: RCSB PDB 5B8B · PDBe 5B8B · UniProt P0AE08 · UniProt P32119
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