Research workbench
Hcmv prefusion gb in complex with fusion inhibitor way-174865
Analyse Hcmv prefusion gb in complex with fusion inhibitor way-174865 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KDP
- Type
- protein
- Length
- 1,914 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B
- UniProt
- P13201
- Ligands
- WCY, NAG, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 24% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope glycoprotein B | protein | 638 | 24% helix, 25% strand | P13201 |
Ligands and binding sites
- WCY · N-{4-[({(1S)-1-[3,5-bis(trifluoromethyl) phenyl]ethyl}carbamothioyl)amino]phenyl}-1,3-thiazole-4-carboxamide · ligand · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.84 | 0.84 | 129 | CA |
| 2 | 565 | 0.84 | 0.89 | 65 | empty |
| 3 | 556 | 0.84 | 0.90 | 66 | empty |
| 4 | 601 | 0.83 | 0.88 | 67 | empty |
| 5 | 131 | 0.78 | 0.96 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6076 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 6034 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 6022 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 glycan, 15 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KDP · HCMV prefusion gB in complex with fusion inhibitor WAY-174865 · 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 7KDP · PDBe 7KDP · UniProt P13201
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