MolNFT v1 · #137431 · protein
Crystal structure of hcmv pentamer in complex with neutralizing antibody 8I21 - low resolution dataset for initial phasing by sad
5VOC · Envelope glycoprotein H: “Crystal structure of hcmv pentamer in complex with neutralizing antibody 8I21 - low resolution dataset for…”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.64). MolNFT v1 #137431…
- PDB
- 5VOC
- Type
- protein
- Length
- 1,706 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Envelope glycoprotein UL128; Envelope…
- UniProt
- Q6SW67, Q68674, P16837, F5HCP3, F5HET4, S6B291, Q6GMX0
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 7 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 662 | 33% helix, 20% strand | Q6SW67 |
| B | Envelope glycoprotein L | protein | 237 | 32% helix, 18% strand | Q68674 |
| C | Envelope glycoprotein UL128 | protein | 135 | 23% helix, 19% strand | P16837 |
| D | Envelope glycoprotein UL130 | protein | 170 | 28% helix, 35% strand | F5HCP3 |
| E | Envelope glycoprotein UL131A | protein | 108 | 43% helix, 18% strand | F5HET4 |
| H | Fab 8I21 heavy chain | protein | 200 | 3% helix, 52% strand | S6B291 |
| L | Fab 8I21 light chain | protein | 194 | 2% helix, 48% strand | Q6GMX0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, E, A, D, H
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.64 | 0.80 | 34 | empty |
| 2 | 409 | 0.57 | 0.74 | 53 | empty |
| 3 | 133 | 0.56 | 0.83 | 23 | empty |
| 4 | 159 | 0.55 | 0.81 | 40 | NAG |
| 5 | 180 | 0.50 | 0.77 | 25 | empty |
Interfaces
11 interfaces between chains.
- A–B · 4114 Ų buried · 47 hydrogen bonds · protein-protein
- D–E · 2715 Ų buried · 41 hydrogen bonds · protein-protein
- H–L · 1684 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1309 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1108 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5VOC · Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 - Low… · 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 Q68674
- Every structure of UniProt P16837
- Every structure of UniProt F5HCP3
- Every structure of UniProt F5HET4
- Every structure of UniProt S6B291
- Every structure of UniProt Q6GMX0
- Elsewhere: RCSB PDB 5VOC · PDBe 5VOC · UniProt Q6SW67 · UniProt Q68674 · UniProt P16837 · UniProt F5HCP3 · UniProt F5HET4 · UniProt S6B291 · UniProt Q6GMX0
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