Research workbench
Crystal structure of the native monooxygenase domain of mical at 1.45 a resolution
Analyse Crystal structure of the native monooxygenase domain of mical at 1.45 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BRY
- Type
- protein
- Length
- 958 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NEDD9 interacting protein with calponin homology and lim domains
- UniProt
- Q8VDP3
- Ligands
- FAD, CL, SO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NEDD9 interacting protein with calponin homology and lim domains | protein | 479 | 39% helix, 21% strand | Q8VDP3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.81 | 0.86 | 92 | FAD |
| 2 | 374 | 0.76 | 0.86 | 64 | FAD |
| 3 | 211 | 0.66 | 0.84 | 48 | empty |
| 4 | 117 | 0.47 | 0.79 | 21 | empty |
| 5 | 103 | 0.43 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 948 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2BRY · Crystal structure of the native monooxygenase domain of MICAL at 1.45 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VDP3 · AlphaFold monomer V2.0 prediction for [F-actin]-monooxygenase MICAL1 (Q8VDP3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8VDP3
- Elsewhere: RCSB PDB 2BRY · PDBe 2BRY · UniProt Q8VDP3
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