MolNFT v1 · #46399 · protein
Human adenovirus type 11 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, mcp)
2O39 · Fiber protein: “Human adenovirus type 11 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, mcp)”. X-ray diffraction, 3 ligands (NAG, BMA, CA), 2 pockets (best druggability 0.65). MolNFT v1 #46399 on…
- 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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