Research workbench
Crystal structure of aclacinomycin oxidoreductase
Analyse Crystal structure of aclacinomycin oxidoreductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IPI
- Type
- protein
- Length
- 1,968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aclacinomycin oxidoreductase (aknox)
- UniProt
- Q0PCD7
- Ligands
- FAD, AKY
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aclacinomycin oxidoreductase (aknox) | protein | 492 | 31% helix, 22% strand | Q0PCD7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- AKY · Methyl (2S,4R)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-4-O-{2,6-dideoxy-4-O-[(2S,6S)-6-methyl-5-oxotetrahydro-2H -pyran-2-yl]-alpha-D-lyxo-hexopyranosyl}-3-(dimethylamino)-D-ribo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-C arboxylate · ligand · chains A
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 | 616 | 0.87 | 0.92 | 96 | FAD |
| 2 | 603 | 0.87 | 0.92 | 91 | FAD |
| 3 | 554 | 0.86 | 0.91 | 66 | FAD |
| 4 | 468 | 0.86 | 0.93 | 70 | FAD |
| 5 | 434 | 0.81 | 0.89 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1439 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1432 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 103 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 2 isopeptide (flavinylation, isopeptide).
Compared structures
- 2IPI · Crystal Structure of Aclacinomycin Oxidoreductase · the same entry in another collection · chain D against D, TM-score 1.00
- Q0PCD7 · AlphaFold monomer V2.0 prediction for aclacinomycin-N/ACLACINOMYCIN-a oxidase (Q0PCD7) · a predicted model of the same protein · chain C 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 Q0PCD7
- Elsewhere: RCSB PDB 2IPI · PDBe 2IPI · UniProt Q0PCD7
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