MolNFT v1 · #140439 · protein
Crystal structure of a human neutralizing antibody bound to a HBV PRES1 peptide
5YAX · SCFV1 antibody: “Crystal structure of a human neutralizing antibody bound to a HBV PRES1 peptide”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.82). MolNFT v1 #140439 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YAX
- Type
- protein
- Length
- 466 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SCFV1 antibody; Large envelope protein
- UniProt
- B2CXZ0
- Ligands
- NA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SCFV1 antibody | protein | 228 | 4% helix, 53% strand | — |
| B | SCFV1 antibody | protein | 230 | 3% helix, 50% strand | — |
| C | Large envelope protein | protein | 8 | 0% helix, 0% strand | B2CXZ0 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.82 | 0.83 | 113 | empty |
| 2 | 89 | 0.41 | 0.78 | 21 | empty |
| 3 | 52 | 0.29 | 0.75 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–B · 886 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YAX · Crystal structure of a human neutralizing antibody bound to a HBV preS1 peptide · 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 B2CXZ0
- Elsewhere: RCSB PDB 5YAX · PDBe 5YAX · UniProt B2CXZ0
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