Research workbench
Cryo-EM reconstruction of a complex of a binding protein and human adenovirus C5 hexon
Analyse Cryo-EM reconstruction of a complex of a binding protein and human adenovirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EQC
- Type
- protein
- Length
- 3,462 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexon protein; Scfv of 9C12 antibody
- UniProt
- P04133
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hexon protein | protein | 921 | 16% helix, 32% strand | P04133 |
| D, E, F | Scfv of 9C12 antibody | protein | 233 | 4% helix, 48% strand | — |
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 | 1075 | 0.79 | 0.81 | 106 | empty |
| 2 | 144 | 0.78 | 0.95 | 27 | empty |
| 3 | 944 | 0.77 | 0.80 | 89 | empty |
| 4 | 423 | 0.75 | 0.84 | 34 | empty |
| 5 | 611 | 0.75 | 0.81 | 45 | empty |
Interfaces
9 interfaces between chains.
- B–C · 9040 Ų buried · 138 hydrogen bonds · protein-protein
- A–C · 8993 Ų buried · 131 hydrogen bonds · protein-protein
- A–B · 8859 Ų buried · 121 hydrogen bonds · protein-protein
- B–E · 601 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 553 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6EQC · Cryo-EM reconstruction of a complex of a binding protein and human adenovirus C5 hexon · the same entry in another collection · chain E against E, 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 6EQC · PDBe 6EQC · UniProt P04133
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