MolNFT v1 · #180796 · protein
Cryoem structure of the hcmv trimer ghglgo in complex with neutralizing fabs 13H11 and msl-109
7LBE · Envelope glycoprotein H: “Cryoem structure of the hcmv trimer ghglgo in complex with neutralizing fabs 13H11 and msl-109”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.73). MolNFT v1 #180796 on…
- PDB
- 7LBE
- Type
- protein
- Length
- 1,653 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Envelope glycoprotein O; Fab 13H11…
- UniProt
- Q6SW67, F5HCH8, Q8BCU3
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 7 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 652 | 33% helix, 21% strand | Q6SW67 |
| B | Envelope glycoprotein L | protein | 234 | 33% helix, 21% strand | F5HCH8 |
| C | Envelope glycoprotein O | protein | 299 | 36% helix, 15% strand | Q8BCU3 |
| E | Fab 13H11 light chain | protein | 107 | 3% helix, 49% strand | — |
| F | Fab 13H11 heavy chain | protein | 121 | 7% helix, 48% strand | — |
| G | Fab msl-109 light chain | protein | 111 | 3% helix, 44% strand | — |
| H | Fab msl-109 heavy chain | protein | 129 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains C, A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C
- BMA · beta-D-mannopyranose · sugar · chains 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.73 | 0.96 | 24 | empty |
| 2 | 169 | 0.71 | 0.89 | 28 | empty |
| 3 | 428 | 0.71 | 0.82 | 54 | empty |
| 4 | 347 | 0.62 | 0.79 | 36 | empty |
| 5 | 165 | 0.57 | 0.81 | 38 | empty |
Interfaces
7 interfaces between chains.
- A–B · 4064 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 2509 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 984 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 963 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 835 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 glycan, 14 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LBE · CryoEM structure of the HCMV Trimer gHgLgO in complex with neutralizing fabs 13H11 and… · 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 Q6SW67
- Every structure of UniProt F5HCH8
- Every structure of UniProt Q8BCU3
- Elsewhere: RCSB PDB 7LBE · PDBe 7LBE · UniProt Q6SW67 · UniProt F5HCH8 · UniProt Q8BCU3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.