MolNFT v1 · #181098 · protein
Crystal structure of pfcsp peptide 21 with vaccine-elicited human anti-malaria antibody M42.127
7LKB · M42.127 Fab heavy chain: “Crystal structure of pfcsp peptide 21 with vaccine-elicited human anti-malaria antibody M42.127”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.76). MolNFT v1 #181098 on GenesisL1: 3D…
- PDB
- 7LKB
- Type
- protein
- Length
- 912 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M42.127 Fab heavy chain; M42.127 Fab light chain; Circumsporozoite protein
- UniProt
- P02893
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | M42.127 Fab heavy chain | protein | 221 | 8% helix, 53% strand | — |
| L | M42.127 Fab light chain | protein | 221 | 6% helix, 52% strand | — |
| A, D | Circumsporozoite protein | protein | 15 | 0% helix, 7% strand | P02893 |
| B | M42.127 Fab heavy chain | protein | 220 | 9% helix, 53% strand | — |
| C | M42.127 Fab light chain | protein | 220 | 6% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.76 | 0.79 | 86 | empty |
| 2 | 1153 | 0.76 | 0.79 | 144 | empty |
| 3 | 293 | 0.70 | 0.84 | 41 | empty |
| 4 | 60 | 0.47 | 0.85 | 21 | empty |
| 5 | 82 | 0.37 | 0.76 | 17 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1885 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1885 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 553 Ų buried · 5 hydrogen bonds · protein-protein
- H–A · 491 Ų buried · 12 hydrogen bonds · protein-protein
- L–A · 488 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7LKB · 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 0.24
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 P02893
- Elsewhere: RCSB PDB 7LKB · PDBe 7LKB · UniProt P02893
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