MolNFT v1 · #105222 · protein
Crystal structure of anti-MSP2 fv fragment (MAB6D8) in complex with 3D7-MSP2 14-30
4QY8 · Fv FRAGMENT(MAB6D8) heavy chain: “Crystal structure of anti-MSP2 fv fragment (MAB6D8) in complex with 3D7-MSP2 14-30”. X-ray diffraction, 1 ligand (ACE), 3 pockets (best druggability 0.31). MolNFT v1 #105222 on GenesisL1: 3D…
- PDB
- 4QY8
- Type
- protein
- Length
- 239 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fv FRAGMENT(MAB6D8) heavy chain; Fv FRAGMENT(MAB6D8) light chain; Merozoite surface…
- UniProt
- P50498
- Ligands
- ACE
- Pockets
- 3 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fv FRAGMENT(MAB6D8) heavy chain | protein | 114 | 8% helix, 52% strand | — |
| B | Fv FRAGMENT(MAB6D8) light chain | protein | 111 | 3% helix, 52% strand | — |
| Q | Merozoite surface antigen 2 | protein | 14 | 0% helix, 0% strand | P50498 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.31 | 0.76 | 15 | empty |
| 2 | 66 | 0.28 | 0.73 | 16 | empty |
| 3 | 54 | 0.25 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 664 Ų buried · 9 hydrogen bonds · protein-protein
- B–Q · 475 Ų buried · 10 hydrogen bonds · protein-protein
- A–Q · 451 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4QY8 · Crystal Structure of anti-MSP2 Fv fragment (mAb6D8) in complex with 3D7-MSP2 14-30 · the same entry in another collection · chain A against A, TM-score 1.00
- P50498 · AlphaFold monomer V2.0 prediction for merozoite surface antigen 2 (P50498) · a predicted model of the same protein · chain Q against A, TM-score 0.24
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 P50498
- Elsewhere: RCSB PDB 4QY8 · PDBe 4QY8 · UniProt P50498
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.