MolNFT v1 · #67336 · protein
Crystal structure of a ternary complex of aklavinone-11 hydroxylase with FAD and aklavinone
3IHG · Rdme: “Crystal structure of a ternary complex of aklavinone-11 hydroxylase with FAD and aklavinone”. X-ray diffraction, 3 ligands (FAD, VAK, SO4), 19 pockets (best druggability 0.83). MolNFT v1 #67336 on GenesisL1: 3D structure…
- PDB
- 3IHG
- Type
- protein
- Length
- 1,605 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rdme
- UniProt
- Q54530
- Ligands
- FAD, VAK, SO4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Rdme | protein | 535 | 31% helix, 27% strand | Q54530 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
- VAK · methyl (1R,2R,4S)-2-ethyl-2,4,5,7-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.83 | 0.85 | 96 | FAD, VAK |
| 2 | 808 | 0.82 | 0.85 | 93 | FAD, VAK |
| 3 | 1065 | 0.82 | 0.83 | 106 | FAD, VAK, SO4 |
| 4 | 78 | 0.75 | 0.98 | 19 | empty |
| 5 | 76 | 0.74 | 0.97 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 387 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 190 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3IHG · Crystal structure of a ternary complex of aklavi -11 hydroxylase with FAD and aklavi · the same entry in another collection · chain A against A, TM-score 1.00
- Q54530 · AlphaFold monomer V2.0 prediction for aklavinone 12-hydroxylase rdme (Q54530) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q54530
- Elsewhere: RCSB PDB 3IHG · PDBe 3IHG · UniProt Q54530
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