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Crystal structure of anti-human cytomegalovirus antibody 8F9 plus gb peptide
Analyse Crystal structure of anti-human cytomegalovirus antibody 8F9 plus gb peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EYF
- Type
- protein
- Length
- 877 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8F9 Fab; Ad-2; Synthetic peptide
- UniProt
- P13201
- Ligands
- NH2
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 8F9 Fab | protein | 215 | 6% helix, 50% strand | — |
| B | Ad-2 | protein | 218 | 8% helix, 51% strand | — |
| D | Ad-2 | protein | 211 | 7% helix, 54% strand | — |
| E, F | Synthetic peptide | protein | 9 | 0% helix, 33% strand | P13201 |
Ligands and binding sites
- NH2 · Amino group · ion · 2 copies · chains B, E, D, F
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.57 | 0.88 | 20 | empty |
| 2 | 321 | 0.54 | 0.75 | 49 | empty |
| 3 | 273 | 0.52 | 0.75 | 34 | empty |
| 4 | 158 | 0.46 | 0.76 | 34 | GOL |
| 5 | 193 | 0.44 | 0.73 | 29 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1646 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1644 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 555 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 536 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 312 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3EYF · Crystal structure of anti-human cytomegalovirus antibody 8f9 plus gB peptide · 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 P13201
- Elsewhere: RCSB PDB 3EYF · PDBe 3EYF · UniProt P13201
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