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Crystal structure of alkyl hydroperoxide reductase from D. radiodurans R1
Analyse Crystal structure of alkyl hydroperoxide reductase from D. radiodurans R1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K40
- Type
- protein
- Length
- 2,225 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyl hydroperoxide reductase ahpd
- EC
- 1.11.1.15
- UniProt
- Q9RTJ7
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, K, L | Alkyl hydroperoxide reductase ahpd (EC 1.11.1.15) | protein | 186 | 73% helix, 0% strand | Q9RTJ7 |
| B, D, E, F, H, I, J | Alkyl hydroperoxide reductase ahpd (EC 1.11.1.15) | protein | 185 | 72% helix, 0% strand | Q9RTJ7 |
Ligands and binding sites
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D, G, E, F, H, I, J, K, L
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, E, J, L
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains G, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.86 | 0.87 | 140 | GOL, PEG |
| 2 | 1135 | 0.85 | 0.86 | 139 | PEG |
| 3 | 251 | 0.83 | 0.96 | 44 | empty |
| 4 | 243 | 0.83 | 0.95 | 38 | empty |
| 5 | 969 | 0.73 | 0.77 | 90 | GOL |
Interfaces
27 interfaces between chains.
- J–L · 2093 Ų buried · 20 hydrogen bonds · protein-protein
- I–K · 2070 Ų buried · 24 hydrogen bonds · protein-protein
- D–G · 2068 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 2052 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 2046 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6K40 · Crystal structure of alkyl hydroperoxide reductase from D. radiodurans R1 · the same entry in another collection · chain J against J, 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 Q9RTJ7
- Elsewhere: RCSB PDB 6K40 · PDBe 6K40 · UniProt Q9RTJ7
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