Research workbench
The quasi-atomic model of the adenovirus type 3 penton dodecahedron
Analyse The quasi-atomic model of the adenovirus type 3 penton dodecahedron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C9F
- Type
- protein
- Length
- 2,250 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penton protein; Fiber
- UniProt
- P03276, Q64831
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Penton protein | protein | 440 | 14% helix, 35% strand | P03276 |
| S, T, U, V, W | Fiber | protein | 10 | 0% helix, 0% strand | Q64831 |
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 | 691 | 0.89 | 0.93 | 121 | empty |
| 2 | 335 | 0.85 | 0.94 | 65 | empty |
| 3 | 372 | 0.84 | 0.93 | 71 | empty |
| 4 | 432 | 0.82 | 0.90 | 35 | empty |
| 5 | 231 | 0.81 | 0.94 | 40 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3210 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 3202 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 3189 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3177 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 3145 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2C9F · The quasi-atomic model of the adenovirus type 3 penton dodecahedron · the same entry in another collection · chain D against D, 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 P03276
- Every structure of UniProt Q64831
- Elsewhere: RCSB PDB 2C9F · PDBe 2C9F · UniProt P03276 · UniProt Q64831
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