Research workbench
Crystal structure of the extracellular domain of glycoprotein B from human cytomegalovirus
Analyse Crystal structure of the extracellular domain of glycoprotein B from human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CXF
- Type
- protein
- Length
- 1,708 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B
- UniProt
- P06473
- Ligands
- NAG, BMA, MAN, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein B | protein | 562 | 20% helix, 39% strand | P06473 |
| B | Envelope glycoprotein B | protein | 570 | 21% helix, 39% strand | P06473 |
| C | Envelope glycoprotein B | protein | 576 | 20% helix, 39% strand | P06473 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- CA · Calcium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.87 | 0.89 | 109 | empty |
| 2 | 375 | 0.81 | 0.90 | 58 | empty |
| 3 | 383 | 0.79 | 0.89 | 57 | empty |
| 4 | 775 | 0.78 | 0.82 | 81 | empty |
| 5 | 854 | 0.75 | 0.79 | 87 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6360 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 6315 Ų buried · 83 hydrogen bonds · protein-protein
- A–C · 6208 Ų buried · 85 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 15 disulfide (N-glycosylation, disulfide).
Compared structures
- 5CXF · Crystal structure of the extracellular domain of glycoprotein B from Human Cytomegalovirus · 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 P06473
- Elsewhere: RCSB PDB 5CXF · PDBe 5CXF · UniProt P06473
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