Research workbench
Cryoem structure of the hcmv trimer ghglgo in complex with human platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and msl-109
Analyse Cryoem structure of the hcmv trimer ghglgo in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LBF
- Type
- protein
- Length
- 1,923 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Envelope glycoprotein O; Isoform 3 of…
- EC
- 2.7.10.1
- UniProt
- Q6SW67, F5HCH8, Q8BCU3, P16234
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 8 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 647 | 34% helix, 20% strand | Q6SW67 |
| B | Envelope glycoprotein L | protein | 236 | 33% helix, 20% strand | F5HCH8 |
| C | Envelope glycoprotein O | protein | 299 | 36% helix, 21% strand | Q8BCU3 |
| D | Isoform 3 of platelet-derived growth factor receptor alpha (EC 2.7.10.1) | protein | 274 | 3% helix, 47% strand | P16234 |
| E | Fab 13H11 light chain | protein | 106 | 3% helix, 47% strand | — |
| F | Fab 13H11 heavy chain | protein | 121 | 5% helix, 52% strand | — |
| G | Fab msl-109 light chain | protein | 111 | 3% helix, 46% 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 · 24 copies · chains C, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.74 | 0.97 | 24 | empty |
| 2 | 433 | 0.72 | 0.82 | 58 | empty |
| 3 | 802 | 0.72 | 0.77 | 70 | empty |
| 4 | 195 | 0.69 | 0.87 | 41 | empty |
| 5 | 160 | 0.66 | 0.87 | 24 | empty |
Interfaces
10 interfaces between chains.
- A–B · 4096 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 2438 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2060 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 961 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 949 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 7LBF · CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth… · the same entry in another collection · chain H against H, TM-score 1.00
- P16234 · AlphaFold monomer V2.0 prediction for platelet-derived growth factor receptor alpha… · a predicted model of the same protein · chain D against A, TM-score 0.63
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 P16234
- Elsewhere: RCSB PDB 7LBF · PDBe 7LBF · UniProt Q6SW67 · UniProt F5HCH8 · UniProt Q8BCU3 · UniProt P16234
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