Research workbench
Crystal structure of 2243 Fab in complex with circumsporozoite protein NANP5
Analyse Crystal structure of 2243 Fab in complex with circumsporozoite protein NANP5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O23
- Type
- protein
- Length
- 885 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2243 Fab heavy chain; 2243 kappa light chain; Circumsporozoite protein
- UniProt
- P02893
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2243 Fab heavy chain | protein | 225 | 7% helix, 49% strand | — |
| B | 2243 kappa light chain | protein | 211 | 6% helix, 51% strand | — |
| C | 2243 Fab heavy chain | protein | 219 | 7% helix, 51% strand | — |
| D | 2243 kappa light chain | protein | 212 | 7% helix, 51% strand | — |
| E | Circumsporozoite protein | protein | 18 | 0% helix, 0% strand | P02893 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, C, E, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.58 | 0.77 | 68 | EDO, SO4 |
| 2 | 407 | 0.55 | 0.73 | 45 | EDO, SO4 |
| 3 | 314 | 0.53 | 0.74 | 41 | empty |
| 4 | 160 | 0.43 | 0.74 | 29 | empty |
| 5 | 90 | 0.36 | 0.75 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1793 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1786 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 555 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 467 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 140 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6O23 · Crystal structure of 2243 Fab in complex with circumsporozoite protein NANP5 · 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 E against A, TM-score 0.27
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 6O23 · PDBe 6O23 · UniProt P02893
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