MolNFT v1 · #167466 · protein
Crystal structure of 4498 Fab in complex with circumsporozoite protein DND3 and anti-kappa vhh domain
6VLN · 4498 Fab heavy chain: “Crystal structure of 4498 Fab in complex with circumsporozoite protein DND3 and anti-kappa vhh domain”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1 #167466 on GenesisL1: 3D structure…
- PDB
- 6VLN
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4498 Fab heavy chain; 4498 Fab light chain; Anti kappa vhh domain; Circumsporozoite…
- UniProt
- P02893
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 4498 Fab heavy chain | protein | 230 | 10% helix, 50% strand | — |
| L | 4498 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| K | Anti kappa vhh domain | protein | 121 | 7% helix, 50% strand | — |
| P | Circumsporozoite protein | protein | 10 | 0% helix, 0% strand | P02893 |
Ligands and binding sites
- GOL · Glycerol · additive · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.70 | 0.77 | 82 | empty |
| 2 | 140 | 0.56 | 0.83 | 38 | empty |
| 3 | 83 | 0.41 | 0.79 | 18 | empty |
| 4 | 101 | 0.37 | 0.75 | 25 | empty |
| 5 | 61 | 0.29 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- H–L · 2138 Ų buried · 28 hydrogen bonds · protein-protein
- H–P · 517 Ų buried · 11 hydrogen bonds · protein-protein
- H–K · 246 Ų buried · 0 hydrogen bonds · protein-protein
- L–P · 166 Ų buried · 4 hydrogen bonds · protein-protein
- L–K · 148 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6VLN · Crystal structure of 4498 Fab in complex with circumsporozoite protein DND3 and… · the same entry in another collection · chain H against H, TM-score 1.00
- P02893 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P02893) · a predicted model of the same protein · chain P against A, TM-score 0.55
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 6VLN · PDBe 6VLN · UniProt P02893
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.