MolNFT v1 · #120414 · protein
Structure of neutralizing antibody bound to zika envelope protein
5GZO · Genome polyprotein: “Structure of neutralizing antibody bound to zika envelope protein”. X-ray diffraction, 19 pockets (best druggability 0.65). MolNFT v1 #120414 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GZO
- Type
- protein
- Length
- 1,634 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Antibody heavy chain; Antibody light chain
- UniProt
- H9A910
- Pockets
- 19 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Genome polyprotein | protein | 390 | 8% helix, 51% strand | H9A910 |
| H, C | Antibody heavy chain | protein | 214 | 6% helix, 49% strand | — |
| L, D | Antibody light chain | protein | 213 | 6% helix, 51% strand | — |
Pockets
19 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.65 | 0.74 | 58 | empty |
| 2 | 661 | 0.64 | 0.74 | 57 | empty |
| 3 | 83 | 0.59 | 0.88 | 24 | empty |
| 4 | 52 | 0.47 | 0.86 | 20 | empty |
| 5 | 132 | 0.47 | 0.78 | 24 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1781 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1750 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 498 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 489 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 375 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5GZO · Structure of neutralizing antibody bound to Zika envelope protein · 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 H9A910
- Elsewhere: RCSB PDB 5GZO · PDBe 5GZO · UniProt H9A910
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