MolNFT v1 · #160905 · protein
Crystal structure of iminodiacetate oxidase (idaa) from chelativorans sp. BNC1
6PXS · FAD dependent oxidoreductase: “Crystal structure of iminodiacetate oxidase (idaa) from chelativorans sp. BNC1”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.84). MolNFT v1 #160905 on GenesisL1: 3D structure…
- PDB
- 6PXS
- Type
- protein
- Length
- 1,478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD dependent oxidoreductase
- UniProt
- Q11HA4
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | FAD dependent oxidoreductase | protein | 370 | 34% helix, 24% strand | Q11HA4 |
| C, D | FAD dependent oxidoreductase | protein | 369 | 34% helix, 24% strand | Q11HA4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.84 | 0.89 | 72 | FAD |
| 2 | 592 | 0.83 | 0.88 | 71 | FAD |
| 3 | 576 | 0.82 | 0.88 | 67 | FAD |
| 4 | 544 | 0.82 | 0.88 | 69 | FAD |
| 5 | 765 | 0.77 | 0.81 | 71 | empty |
Interfaces
6 interfaces between chains.
- B–D · 878 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 851 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 849 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 750 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6PXS · Crystal structure of iminodiacetate oxidase (IdaA) from Chelativorans sp. BNC1 · the same entry in another collection · chain A 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 Q11HA4
- Elsewhere: RCSB PDB 6PXS · PDBe 6PXS · UniProt Q11HA4
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