MolNFT v1 · #137739 · protein
The antigen-binding fragment of MAB24 in complex with a peptide from hepatitis C virus E2 epitope I (412-423)
5VXR · MAB24 variable heavy CHAIN,MAB24 variable heavy chain: “The antigen-binding fragment of MAB24 in complex with a peptide from hepatitis C virus E2 epitope I (412-423)”. X-ray diffraction, 4 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 5VXR
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAB24 variable heavy CHAIN,MAB24 variable heavy chain; MAB24 variable light CHAIN,MAB24…
- UniProt
- Q569X1, A0A125T908, Q5EG65
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | MAB24 variable heavy CHAIN,MAB24 variable heavy chain | protein | 207 | 3% helix, 56% strand | Q569X1 |
| L | MAB24 variable light CHAIN,MAB24 variable light chain | protein | 217 | 6% helix, 52% strand | A0A125T908 |
| P | Virus envelope protein 2 | protein | 10 | 0% helix, 60% strand | Q5EG65 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains H, P, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.64 | 0.75 | 57 | GOL |
| 2 | 96 | 0.34 | 0.73 | 24 | GOL |
| 3 | 50 | 0.26 | 0.74 | 15 | empty |
| 4 | 52 | 0.26 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1866 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 310 Ų buried · 5 hydrogen bonds · protein-protein
- L–P · 305 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5VXR · The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2… · the same entry in another collection · chain H against H, 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 Q569X1
- Every structure of UniProt A0A125T908
- Every structure of UniProt Q5EG65
- Elsewhere: RCSB PDB 5VXR · PDBe 5VXR · UniProt Q569X1 · UniProt A0A125T908 · UniProt Q5EG65
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