Research workbench
Human adenovirus type 11 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, mcp)
Analyse Human adenovirus type 11 knob in complex with domains SCR1 and SCR2 of CD46… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O39
- Type
- protein
- Length
- 646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein; Membrane cofactor protein
- UniProt
- P35774, P15529
- Ligands
- NAG, BMA, CA
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fiber protein | protein | 197 | 8% helix, 40% strand | P35774 |
| C, D | Membrane cofactor protein | protein | 126 | 0% helix, 37% strand | P15529 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.65 | 0.77 | 50 | empty |
| 2 | 507 | 0.64 | 0.76 | 52 | empty |
Interfaces
2 interfaces between chains.
- A–C · 602 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 597 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2O39 · Human Adenovirus type 11 knob in complex with domains SCR1 and SCR2 of CD46 (membrane… · the same entry in another collection · chain A against A, TM-score 1.00
- P15529 · AlphaFold monomer V2.0 prediction for membrane cofactor protein (P15529) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 P35774
- Every structure of UniProt P15529
- Elsewhere: RCSB PDB 2O39 · PDBe 2O39 · UniProt P35774 · UniProt P15529
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