Research workbench
Cryoem structure of the plasmodium berghei circumsporozoite protein in complex with inhibitory mouse antibody 3D11.
Analyse Cryoem structure of the plasmodium berghei circumsporozoite protein in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X87
- Type
- protein
- Length
- 3,085 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3D11 Fab heavy chain; 3D11 Fab kappa chain; Circumsporozoite protein
- UniProt
- D1L8V5
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, M, I, G, E, C, A | 3D11 Fab heavy chain | protein | 213 | 4% helix, 48% strand | — |
| L, N, J, H, F, D, B | 3D11 Fab kappa chain | protein | 219 | 5% helix, 44% strand | — |
| X | Circumsporozoite protein | protein | 61 | 0% helix, 0% strand | D1L8V5 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.78 | 0.81 | 91 | empty |
| 2 | 788 | 0.76 | 0.81 | 76 | empty |
| 3 | 523 | 0.76 | 0.84 | 57 | empty |
| 4 | 484 | 0.74 | 0.83 | 65 | empty |
| 5 | 437 | 0.74 | 0.83 | 59 | empty |
Interfaces
50 interfaces between chains.
- C–D · 1892 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 1887 Ų buried · 9 hydrogen bonds · protein-protein
- M–N · 1886 Ų buried · 7 hydrogen bonds · protein-protein
- K–L · 1862 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1862 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide (disulfide).
Compared structures
- 6X87 · CryoEM structure of the Plasmodium berghei circumsporozoite protein in complex with… · the same entry in another collection · chain N against N, 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 D1L8V5
- Elsewhere: RCSB PDB 6X87 · PDBe 6X87 · UniProt D1L8V5
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