MolNFT v1 · #158711 · protein
Crystal structure of 3246 Fab in complex with circumsporozoite protein nana
6O26 · 3246 Fab heavy chain: “Crystal structure of 3246 Fab in complex with circumsporozoite protein nana”. X-ray diffraction, 4 pockets (best druggability 0.55). MolNFT v1 #158711 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6O26
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3246 Fab heavy chain; 3246 Fab light chain; Circumsporozoite protein
- UniProt
- P19597
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3246 Fab heavy chain | protein | 215 | 8% helix, 51% strand | — |
| B | 3246 Fab light chain | protein | 213 | 7% helix, 50% strand | — |
| C | Circumsporozoite protein | protein | 10 | 0% helix, 0% strand | P19597 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B, C
- IPA · Isopropyl alcohol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.55 | 0.74 | 45 | empty |
| 2 | 146 | 0.43 | 0.75 | 31 | empty |
| 3 | 70 | 0.28 | 0.73 | 14 | empty |
| 4 | 51 | 0.25 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1644 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 454 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 159 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6O26 · Crystal structure of 3246 Fab in complex with circumsporozoite protein NANA · the same entry in another collection · chain A against A, TM-score 1.00
- P19597 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P19597) · a predicted model of the same protein · chain C against A, TM-score 0.45
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 6O26 · PDBe 6O26 · UniProt P19597
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