Research workbench
Cryoem structure of the hcmv pentamer GH/GL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 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
- 7T4Q
- Type
- protein
- Length
- 1,946 residues
- Chains
- 11
- 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
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 11 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 623 | 34% helix, 19% strand | F5H9T3 |
| B | Envelope glycoprotein L | protein | 233 | 36% helix, 19% strand | Q71DN9 |
| C | Envelope protein UL128 | protein | 124 | 27% helix, 22% strand | Q38LY2 |
| D | Envelope glycoprotein UL130 | protein | 164 | 26% helix, 35% strand | Q38M07 |
| E | Envelope protein UL131A | protein | 111 | 43% helix, 21% strand | Q8AZ45 |
| F | Fab 2C12 heavy chain | protein | 124 | 5% helix, 50% strand | — |
| G | Fab 2C12 light chain | protein | 112 | 3% helix, 50% strand | — |
| H | Fab 7I13 light chain | protein | 107 | 6% helix, 49% strand | — |
| I | Fab 7I13 heavy chain | protein | 122 | 9% helix, 50% strand | — |
| J | Fab 13H11 heavy chain | protein | 121 | 7% helix, 50% strand | — |
| K | Fab 13H11 light chain | protein | 105 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D, E, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.72 | 0.84 | 62 | empty |
| 2 | 381 | 0.69 | 0.82 | 50 | empty |
| 3 | 226 | 0.56 | 0.79 | 37 | empty |
| 4 | 59 | 0.54 | 0.88 | 24 | empty |
| 5 | 72 | 0.54 | 0.86 | 15 | empty |
Interfaces
19 interfaces between chains.
- A–B · 3969 Ų buried · 51 hydrogen bonds · protein-protein
- D–E · 2818 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1259 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 993 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 956 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7T4Q · CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with… · 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 F5H9T3
- Every structure of UniProt Q71DN9
- Every structure of UniProt Q38LY2
- Every structure of UniProt Q38M07
- Every structure of UniProt Q8AZ45
- Elsewhere: RCSB PDB 7T4Q · PDBe 7T4Q · UniProt F5H9T3 · UniProt Q71DN9 · UniProt Q38LY2 · UniProt Q38M07 · UniProt Q8AZ45
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