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Cryo-EM structure of the circumsporozoite protein of plasmodium falciparum with a vaccine-elicited antibody reveals maturation of inter-antibody contacts
Analyse Cryo-EM structure of the circumsporozoite protein of plasmodium falciparum with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MB3
- Type
- protein
- Length
- 2,178 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmodium falciparum recombinant shortened csp; FAB311 heavy chain; FAB311 light chain
- UniProt
- P0DOX5
- Pockets
- 20 · best druggability 0.67
Structure
electron microscopy · 3 distinct chains · 4% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Plasmodium falciparum recombinant shortened csp | protein | 90 | 0% helix, 0% strand | — |
| H, A, B, C, D, F, G, I, J | FAB311 heavy chain | protein | 120 | 8% helix, 54% strand | P0DOX5 |
| L, K, M, N, O, P, Q, R, S | FAB311 light chain | protein | 112 | 3% helix, 45% strand | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.67 | 0.78 | 71 | empty |
| 2 | 513 | 0.67 | 0.78 | 73 | empty |
| 3 | 488 | 0.67 | 0.78 | 58 | empty |
| 4 | 515 | 0.67 | 0.78 | 64 | empty |
| 5 | 542 | 0.66 | 0.77 | 70 | empty |
Interfaces
52 interfaces between chains.
- I–R · 998 Ų buried · 13 hydrogen bonds · protein-protein
- C–N · 977 Ų buried · 14 hydrogen bonds · protein-protein
- D–O · 976 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 974 Ų buried · 13 hydrogen bonds · protein-protein
- J–S · 968 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 6MB3 · Cryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a… · the same entry in another collection · chain E against E, 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 P0DOX5
- Elsewhere: RCSB PDB 6MB3 · PDBe 6MB3 · UniProt P0DOX5
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