Research workbench
Crystal structure of pfcsp peptide 21 with vaccine-elicited human anti-malaria antibody M42.126
Analyse Crystal structure of pfcsp peptide 21 with vaccine-elicited human anti-malaria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RD3
- Type
- protein
- Length
- 898 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody M42.126 heavy chain; Antibody M42.126 light chain; Circumsporozoite protein
- UniProt
- P02893
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody M42.126 heavy chain | protein | 215 | 7% helix, 53% strand | — |
| B, L | Antibody M42.126 light chain | protein | 217 | 6% helix, 53% strand | — |
| H | Antibody M42.126 heavy chain | protein | 220 | 8% helix, 54% strand | — |
| C | Circumsporozoite protein | protein | 15 | 0% helix, 7% strand | P02893 |
| D | Circumsporozoite protein | protein | 14 | 0% helix, 7% strand | P02893 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.72 | 0.80 | 63 | empty |
| 2 | 730 | 0.67 | 0.75 | 63 | empty |
| 3 | 665 | 0.64 | 0.74 | 65 | empty |
| 4 | 55 | 0.51 | 0.87 | 21 | empty |
| 5 | 61 | 0.25 | 0.72 | 13 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1935 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1692 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 485 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 471 Ų buried · 12 hydrogen bonds · protein-protein
- L–D · 442 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7RD3 · Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody… · the same entry in another collection · chain D against D, TM-score 1.00
- P02893 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P02893) · a predicted model of the same protein · chain D against A, TM-score 0.30
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 P02893
- Elsewhere: RCSB PDB 7RD3 · PDBe 7RD3 · UniProt P02893
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