Research workbench
Crystal structure of 3D11 Fab in complex with plasmodium berghei circumsporozoite protein mixed peptide
Analyse Crystal structure of 3D11 Fab in complex with plasmodium berghei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X8U
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3D11 Fab heavy chain; 3D11 Fab light chain; Mixed peptide
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 3D11 Fab heavy chain | protein | 214 | 8% helix, 50% strand | — |
| L | 3D11 Fab light chain | protein | 219 | 6% helix, 52% strand | — |
| P | Mixed peptide | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 10 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.56 | 0.74 | 45 | GOL |
| 2 | 53 | 0.51 | 0.88 | 20 | GOL |
| 3 | 120 | 0.38 | 0.74 | 30 | GOL |
| 4 | 63 | 0.30 | 0.75 | 17 | GOL |
Interfaces
3 interfaces between chains.
- H–L · 1816 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 447 Ų buried · 10 hydrogen bonds · protein-protein
- L–P · 399 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6X8U · Crystal structure of 3D11 Fab in complex with Plasmodium berghei circumsporozoite protein… · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 6X8U · PDBe 6X8U
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