Research workbench
Cryoem structure of the hcmv pentamer GH/GL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11
Analyse Cryoem structure of the hcmv pentamer GH/GL/UL128/UL130/UL131A in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T4S
- Type
- protein
- Length
- 2,045 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Envelope protein UL128; Envelope…
- UniProt
- F5H9T3, Q71DN9, Q38LY2, Q38M07, Q8AZ45, O60462
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.71
Structure
electron microscopy · 10 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 624 | 34% helix, 20% strand | F5H9T3 |
| B | Envelope glycoprotein L | protein | 227 | 36% helix, 20% strand | Q71DN9 |
| C | Envelope protein UL128 | protein | 112 | 25% helix, 18% strand | Q38LY2 |
| D | Envelope glycoprotein UL130 | protein | 166 | 27% helix, 34% strand | Q38M07 |
| E | Envelope protein UL131A | protein | 99 | 49% helix, 18% strand | Q8AZ45 |
| F | Neuropilin-2 | protein | 363 | 4% helix, 47% strand | O60462 |
| H | Fab 8I21 heavy chain | protein | 121 | 2% helix, 55% strand | — |
| J | Fab 13H11 heavy chain | protein | 121 | 5% helix, 50% strand | — |
| K | Fab 13H11 light chain | protein | 105 | 3% helix, 44% strand | — |
| I | Fab 8I21 light chain | protein | 107 | 3% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, D, H, I, C, E, F
- CA · Calcium ion · metal · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.71 | 0.95 | 25 | empty |
| 2 | 864 | 0.69 | 0.75 | 67 | empty |
| 3 | 432 | 0.68 | 0.80 | 52 | empty |
| 4 | 147 | 0.67 | 0.88 | 20 | empty |
| 5 | 141 | 0.56 | 0.82 | 29 | empty |
Interfaces
17 interfaces between chains.
- A–B · 4155 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 2639 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1230 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 976 Ų buried · 13 hydrogen bonds · protein-protein
- A–K · 961 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7T4S · CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and… · the same entry in another collection · chain I against I, TM-score 1.00
- O60462 · AlphaFold monomer V2.0 prediction for neuropilin-2 (O60462) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 F5H9T3
- Every structure of UniProt Q71DN9
- Every structure of UniProt Q38LY2
- Every structure of UniProt Q38M07
- Every structure of UniProt Q8AZ45
- Every structure of UniProt O60462
- Elsewhere: RCSB PDB 7T4S · PDBe 7T4S · UniProt F5H9T3 · UniProt Q71DN9 · UniProt Q38LY2 · UniProt Q38M07 · UniProt Q8AZ45 · UniProt O60462
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