MolNFT v1 · #169317 · protein
Cryoem structure of the plasmodium berghei circumsporozoite protein in complex with inhibitory mouse antibody 3D11.
6X87 · 3D11 Fab heavy chain: “Cryoem structure of the plasmodium berghei circumsporozoite protein in complex with inhibitory mouse antibody…”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #169317 on GenesisL1: 3D…
- 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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