Research workbench
Structure of pfcsp peptide 25 with human antibody CIS42
Analyse Structure of pfcsp peptide 25 with human antibody CIS42 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B5S
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CIS42 Fab heavy chain; CIS42 Fab light chain; Pfcsp peptide 25…
- Ligands
- NA, NH4
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CIS42 Fab heavy chain | protein | 216 | 8% helix, 52% strand | — |
| L | CIS42 Fab light chain | protein | 212 | 8% helix, 50% strand | — |
| A | Pfcsp peptide 25: asn-val-asp-pro-asn-ala-asn-pro-asn-val- asp-pro-asn | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 13 copies · chains H, L
- NH4 · Ammonium ion · ion · 26 copies · chains H, L, A
- IPA · Isopropyl alcohol · additive · 9 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.45 | 0.73 | 29 | IPA, NA |
| 2 | 102 | 0.35 | 0.74 | 23 | NH4 |
| 3 | 50 | 0.30 | 0.77 | 16 | NH4, NA |
| 4 | 58 | 0.26 | 0.73 | 16 | NH4, NA |
Interfaces
3 interfaces between chains.
- H–L · 1670 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 442 Ų buried · 15 hydrogen bonds · protein-protein
- L–A · 206 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 6B5S · Structure of PfCSP peptide 25 with human antibody CIS42 · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6B5S · PDBe 6B5S
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