Research workbench
Cryoem structure of the hcmv trimer ghglgo in complex with human transforming growth factor beta receptor type 3 and neutralizing fabs 13H11 and msl-109
Analyse Cryoem structure of the hcmv trimer ghglgo in complex with human transforming… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LBG
- Type
- protein
- Length
- 1,788 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Envelope glycoprotein O; Transforming…
- UniProt
- Q6SW67, F5HCH8, Q8BCU3, Q03167
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 8 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 635 | 33% helix, 21% strand | Q6SW67 |
| B | Envelope glycoprotein L | protein | 234 | 32% helix, 21% strand | F5HCH8 |
| C | Envelope glycoprotein O | protein | 296 | 38% helix, 23% strand | Q8BCU3 |
| D | Transforming growth factor beta receptor type 3 | protein | 156 | 13% helix, 39% strand | Q03167 |
| E | Fab 13H11 light chain | protein | 106 | 3% helix, 47% strand | — |
| F | Fab 13H11 heavy chain | protein | 121 | 5% helix, 48% strand | — |
| G | Fab msl-109 light chain | protein | 111 | 3% helix, 50% strand | — |
| H | Fab msl-109 heavy chain | protein | 129 | 2% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 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 | 910 | 0.75 | 0.78 | 101 | empty |
| 2 | 101 | 0.73 | 0.95 | 24 | empty |
| 3 | 412 | 0.72 | 0.83 | 49 | empty |
| 4 | 131 | 0.64 | 0.87 | 24 | empty |
| 5 | 52 | 0.59 | 0.91 | 18 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4059 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 2492 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 976 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 964 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 838 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 13 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LBG · CryoEM structure of the HCMV Trimer gHgLgO in complex with human Transforming growth… · the same entry in another collection · chain H against H, TM-score 1.00
- Q03167 · AlphaFold monomer V2.0 prediction for transforming growth factor beta receptor type 3… · a predicted model of the same protein · chain D against A, TM-score 0.98
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
- Every structure of UniProt Q03167
- Elsewhere: RCSB PDB 7LBG · PDBe 7LBG · UniProt Q6SW67 · UniProt F5HCH8 · UniProt Q8BCU3 · UniProt Q03167
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