Research workbench
Anti-human cytomegalovirus (hcmv) Fab KE5 with epitope peptide ad-2S1
Analyse Anti-human cytomegalovirus (hcmv) Fab KE5 with epitope peptide ad-2S1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HHA
- Type
- protein
- Length
- 448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab KE5; Antibody KE5; Glycoprotein B
- UniProt
- Q9YKI2
- Ligands
- CL
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab KE5 | protein | 212 | 6% helix, 50% strand | — |
| B | Antibody KE5 | protein | 226 | 11% helix, 51% strand | — |
| P | Glycoprotein B | protein | 10 | 0% helix, 40% strand | Q9YKI2 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, P, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.47 | 0.74 | 36 | empty |
| 2 | 99 | 0.38 | 0.76 | 19 | empty |
| 3 | 86 | 0.38 | 0.76 | 15 | empty |
| 4 | 70 | 0.35 | 0.76 | 20 | empty |
| 5 | 86 | 0.34 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1957 Ų buried · 17 hydrogen bonds · protein-protein
- B–P · 717 Ų buried · 15 hydrogen bonds · protein-protein
- A–P · 347 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4HHA · Anti-Human Cytomegalovirus (HCMV) Fab KE5 with epitope peptide AD-2S1 · 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 Q9YKI2
- Elsewhere: RCSB PDB 4HHA · PDBe 4HHA · UniProt Q9YKI2
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