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Crystal structure of the 2-hydrazinopyridine of semicarbazide- sensitive amine oxidase
Analyse Crystal structure of the 2-hydrazinopyridine of semicarbazide- sensitive amine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C11
- Type
- protein
- Length
- 2,684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane copper amine oxidase
- EC
- 1.4.3.6
- UniProt
- Q16853
- Ligands
- NAG, FUC, BMA, MAN, CU, CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Membrane copper amine oxidase (EC 1.4.3.6) | protein | 671 | 14% helix, 41% strand | Q16853 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CU · Copper (II) ion · metal · 30 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.86 | 0.87 | 89 | empty |
| 2 | 1182 | 0.85 | 0.86 | 99 | empty |
| 3 | 448 | 0.80 | 0.88 | 59 | CU |
| 4 | 442 | 0.78 | 0.86 | 50 | empty |
| 5 | 427 | 0.78 | 0.87 | 50 | CU |
Interfaces
2 interfaces between chains.
- C–D · 7604 Ų buried · 116 hydrogen bonds · protein-protein
- A–B · 7575 Ų buried · 118 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 8 disulfide, 4 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 2C11 · Crystal structure of the 2-hydrazinopyridine of semicarbazide- sensitive amine oxidase · the same entry in another collection · chain D against D, TM-score 1.00
- Q16853 · AlphaFold monomer V2.0 prediction for membrane primary amine oxidase (Q16853) · a predicted model of the same protein · chain D 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 Q16853
- Elsewhere: RCSB PDB 2C11 · PDBe 2C11 · UniProt Q16853
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