MolNFT v1 · #120413 · protein
Structure of neutralizing antibody bound to zika envelope protein
5GZN · Genome polyprotein: “Structure of neutralizing antibody bound to zika envelope protein”. X-ray diffraction, 19 pockets (best druggability 0.75). MolNFT v1 #120413 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GZN
- Type
- protein
- Length
- 2,044 residues
- Chains
- 8
- 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 0.75
Structure
x-ray diffraction · 8 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 402 | 7% helix, 48% strand | H9A910 |
| H | Antibody heavy chain | protein | 224 | 6% helix, 48% strand | — |
| L | Antibody light chain | protein | 213 | 8% helix, 51% strand | — |
| B | Genome polyprotein | protein | 401 | 7% helix, 48% strand | H9A910 |
| C | Antibody heavy chain | protein | 223 | 9% helix, 48% strand | — |
| D | Antibody light chain | protein | 214 | 8% helix, 50% strand | — |
| E | Genome polyprotein | protein | 184 | 11% helix, 46% strand | H9A910 |
| G | Genome polyprotein | protein | 183 | 11% helix, 46% strand | H9A910 |
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.75 | 0.79 | 113 | empty |
| 2 | 968 | 0.70 | 0.75 | 86 | empty |
| 3 | 772 | 0.68 | 0.76 | 75 | empty |
| 4 | 203 | 0.68 | 0.86 | 38 | empty |
| 5 | 582 | 0.63 | 0.75 | 67 | empty |
Interfaces
16 interfaces between chains.
- C–D · 1833 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1786 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 693 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 681 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 536 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide (disulfide).
Compared structures
- 5GZN · 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 5GZN · PDBe 5GZN · UniProt H9A910
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