Research workbench
Crystal structure of pfeba-175 rii in complex with a Fab fragment from inhibitory antibody R217
Analyse Crystal structure of pfeba-175 rii in complex with a Fab fragment from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QEX
- Type
- protein
- Length
- 1,982 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythrocyte-binding antigen-175; Antibody light chain; Antibody heavy chain
- UniProt
- Q05644
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythrocyte-binding antigen-175 | protein | 561 | 62% helix, 2% strand | Q05644 |
| L | Antibody light chain | protein | 212 | 3% helix, 48% strand | — |
| H | Antibody heavy chain | protein | 206 | 1% helix, 50% strand | — |
| B | Erythrocyte-binding antigen-175 | protein | 580 | 62% helix, 2% strand | Q05644 |
| M | Antibody light chain | protein | 213 | 5% helix, 47% strand | — |
| I | Antibody heavy chain | protein | 210 | 1% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.74 | 0.77 | 86 | empty |
| 2 | 753 | 0.69 | 0.76 | 66 | empty |
| 3 | 669 | 0.65 | 0.75 | 64 | empty |
| 4 | 154 | 0.65 | 0.86 | 25 | empty |
| 5 | 157 | 0.65 | 0.86 | 26 | empty |
Interfaces
7 interfaces between chains.
- M–I · 1645 Ų buried · 14 hydrogen bonds · protein-protein
- L–H · 1565 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 503 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 462 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 273 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide (disulfide).
Compared structures
- 4QEX · Crystal structure of PfEBA-175 RII in complex with a Fab fragment from inhibitory… · 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 Q05644
- Elsewhere: RCSB PDB 4QEX · PDBe 4QEX · UniProt Q05644
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