Research workbench
Complex of a binding protein and human adenovirus C 5 hexon
Analyse Complex of a binding protein and human adenovirus C 5 hexon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OGI
- Type
- protein
- Length
- 1,154 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexon protein; Scfv of 9C12 antibody
- UniProt
- P04133
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hexon protein | protein | 921 | 17% helix, 30% strand | P04133 |
| B | Scfv of 9C12 antibody | protein | 233 | 4% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A
- DIO · 1,4-diethylene dioxide · additive · 10 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.76 | 0.85 | 46 | empty |
| 2 | 356 | 0.65 | 0.80 | 39 | empty |
| 3 | 436 | 0.65 | 0.77 | 34 | MES |
| 4 | 318 | 0.59 | 0.77 | 33 | empty |
| 5 | 266 | 0.59 | 0.79 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5OGI · Complex of a binding protein and human adenovirus C 5 hexon · 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 P04133
- Elsewhere: RCSB PDB 5OGI · PDBe 5OGI · UniProt P04133
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