MolNFT v1 · #158712 · protein
Crystal structure of 4493 Fab in complex with circumsporozoite protein kqpa and anti-kappa vhh domain
6O28 · 4493 Fab heavy chain: “Crystal structure of 4493 Fab in complex with circumsporozoite protein kqpa and anti-kappa vhh domain”. X-ray diffraction, 15 pockets (best druggability 0.70). MolNFT v1 #158712 on GenesisL1: 3D structure…
- PDB
- 6O28
- Type
- protein
- Length
- 1,120 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4493 Fab heavy chain; 4493 kappa light chain; Circumsporozoite protein; Anti-kappa vhh…
- UniProt
- P19597
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4493 Fab heavy chain | protein | 218 | 10% helix, 50% strand | — |
| B, D | 4493 kappa light chain | protein | 214 | 7% helix, 52% strand | — |
| C | 4493 Fab heavy chain | protein | 216 | 10% helix, 51% strand | — |
| E, F | Circumsporozoite protein | protein | 10 | 0% helix, 0% strand | P19597 |
| G | Anti-kappa vhh domain | protein | 117 | 5% helix, 52% strand | — |
| K | Anti-kappa vhh domain | protein | 121 | 7% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.70 | 0.78 | 68 | empty |
| 2 | 72 | 0.67 | 0.94 | 30 | empty |
| 3 | 87 | 0.66 | 0.92 | 34 | empty |
| 4 | 597 | 0.66 | 0.76 | 75 | empty |
| 5 | 64 | 0.59 | 0.90 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1763 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1719 Ų buried · 12 hydrogen bonds · protein-protein
- D–K · 601 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 597 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 471 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6O28 · Crystal structure of 4493 Fab in complex with circumsporozoite protein KQPA and… · the same entry in another collection · chain K against K, TM-score 1.00
- P19597 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P19597) · a predicted model of the same protein · chain F against A, TM-score 0.34
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 P19597
- Elsewhere: RCSB PDB 6O28 · PDBe 6O28 · UniProt P19597
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