MolNFT v1 · #114295 · protein
Crystal structure of oxidized chimeric ECAHPC1-186-yfskhn
5B8A · Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2: “Crystal structure of oxidized chimeric ECAHPC1-186-yfskhn”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.73). MolNFT v1 #114295 on GenesisL1: 3D…
- PDB
- 5B8A
- Type
- protein
- Length
- 1,668 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
- 20 · best druggability 0.73
Structure
x-ray diffraction · 9 distinct chains · 31% 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 | 168 | 31% helix, 29% strand | P0AE08, P32119 |
| B | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 166 | 32% helix, 28% strand | P0AE08, P32119 |
| C | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 163 | 33% helix, 29% strand | P0AE08, P32119 |
| D, I | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 162 | 33% helix, 28% strand | P0AE08, P32119 |
| E | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 164 | 31% helix, 29% strand | P0AE08, P32119 |
| F | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 165 | 32% helix, 29% strand | P0AE08, P32119 |
| G | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 171 | 31% helix, 28% strand | P0AE08, P32119 |
| H | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 177 | 30% helix, 27% strand | P0AE08, P32119 |
| J | Alkyl hydroperoxide reductase subunit C,PEROXIREDOXIN-2 (EC 1.11.1.15) | protein | 170 | 30% helix, 28% strand | P0AE08, P32119 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 23 copies · chains A, F, B, C, D, E, J, G, H, I
- GOL · Glycerol · additive · 22 copies · chains A, B, C, D, E, J, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.73 | 0.92 | 19 | empty |
| 2 | 97 | 0.72 | 0.94 | 22 | empty |
| 3 | 123 | 0.71 | 0.91 | 20 | GOL |
| 4 | 116 | 0.71 | 0.91 | 22 | GOL |
| 5 | 117 | 0.70 | 0.91 | 20 | empty |
Interfaces
10 interfaces between chains.
- H–I · 1460 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1364 Ų buried · 17 hydrogen bonds · protein-protein
- E–J · 1331 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1268 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1099 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- P0AE08 · AlphaFold monomer V2.0 prediction for alkyl hydroperoxide reductase C (P0AE08) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P32119 · AlphaFold monomer V2.0 prediction for peroxiredoxin-2 (P32119) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 5B8A · PDBe 5B8A · UniProt P0AE08 · UniProt P32119
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