Research workbench
Crystal structure of 4493 Fab in complex with circumsporozoite protein NANP3 and anti-kappa VHH domain
Analyse Crystal structure of 4493 Fab in complex with circumsporozoite protein NANP3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O2C
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.017
- Source
- Homo sapiens; Lama glama; SYNTHETIC CONSTRUCT
- Molecule
- 4493 Fab heavy chain; 4493 Kappa light chain; Anti-kappa VHH domain; Circumsporozoite…
- UniProt
- P02893
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.017 · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4493 Fab heavy chain | protein | 225 | 8% helix, 49% strand | — |
| B | 4493 Kappa light chain | protein | 215 | 7% helix, 53% strand | — |
| K | Anti-kappa VHH domain | protein | 121 | 2% helix, 50% strand | — |
| C | Circumsporozoite protein | protein | 11 | 27% helix, 0% strand | P02893 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.66 | 0.94 | 30 | empty |
| 2 | 114 | 0.55 | 0.84 | 32 | empty |
| 3 | 67 | 0.55 | 0.88 | 20 | EDO |
| 4 | 183 | 0.55 | 0.80 | 33 | empty |
| 5 | 246 | 0.48 | 0.73 | 36 | PGE |
Interfaces
4 interfaces between chains.
- A–B · 2063 Ų buried · 20 hydrogen bonds · protein-protein
- B–K · 640 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 200 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6O2C · Crystal structure of 4493 Fab in complex with circumsporozoite protein NANP3 and… · the same entry in another collection · chain A against A, TM-score 1.00
- P02893 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P02893) · a predicted model of the same protein · chain C against A, TM-score 0.43
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 6O2C · PDBe 6O2C · UniProt P02893
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