MolNFT v1 · #172952 · protein
Crystal structure of human adenovirus 56 fiber knob
7AJP: “Crystal structure of human adenovirus 56 fiber knob”. X-ray diffraction, 1 ligand (NO3), 12 pockets (best druggability 0.78). MolNFT v1 #172952 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7AJP
- Type
- protein
- Length
- 2,215 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber
- UniProt
- R9RU05
- Ligands
- NO3
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, I, K | Fiber | protein | 186 | 3% helix, 45% strand | R9RU05 |
| B, G | Fiber | protein | 184 | 5% helix, 45% strand | R9RU05 |
| D, J | Fiber | protein | 185 | 3% helix, 44% strand | R9RU05 |
| F | Fiber | protein | 181 | 5% helix, 46% strand | R9RU05 |
| H, L | Fiber | protein | 183 | 5% helix, 45% strand | R9RU05 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 5 copies · chains A, B, D, E
- EDO · 1,2-ethanediol · additive · 33 copies · chains A, C, B, D, E, F, G, H, I
- GOL · Glycerol · additive · 18 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- PGE · Triethylene glycol · additive · 5 copies · chains A, C, D, E, B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.78 | 0.80 | 109 | EDO, NO3, GOL |
| 2 | 363 | 0.73 | 0.84 | 42 | GOL, NO3 |
| 3 | 343 | 0.71 | 0.83 | 39 | GOL |
| 4 | 353 | 0.71 | 0.83 | 38 | GOL |
| 5 | 380 | 0.71 | 0.83 | 41 | GOL |
Interfaces
22 interfaces between chains.
- D–E · 1084 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1080 Ų buried · 23 hydrogen bonds · protein-protein
- G–I · 1069 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1066 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1059 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7AJP · Crystal Structure of Human Adenovirus 56 Fiber Knob · 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 R9RU05
- Elsewhere: RCSB PDB 7AJP · PDBe 7AJP · UniProt R9RU05
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