MolNFT v1 · #186334 · protein
Structure of pfcsp peptide 21 with antibody igl-CIS43.D3
7RAJ · Igl-CIS43.D3 Fab heavy chain: “Structure of pfcsp peptide 21 with antibody igl-CIS43.D3”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.46). MolNFT v1 #186334 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7RAJ
- Type
- protein
- Length
- 451 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Igl-CIS43.D3 Fab heavy chain; Igl-CIS43.D3 Fab light chain…
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Igl-CIS43.D3 Fab heavy chain | protein | 221 | 5% helix, 52% strand | — |
| L | Igl-CIS43.D3 Fab light chain | protein | 217 | 6% helix, 50% strand | — |
| A | Asn-pro-asp-pro-asn-ala-asn-pro-asn-val-asp-pro-asn-ala- asn | protein | 13 | 0% helix, 8% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains H, L
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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 | 173 | 0.46 | 0.76 | 25 | MES |
| 2 | 50 | 0.30 | 0.76 | 14 | empty |
| 3 | 51 | 0.29 | 0.76 | 15 | empty |
| 4 | 51 | 0.25 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1946 Ų buried · 22 hydrogen bonds · protein-protein
- H–A · 448 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 380 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7RAJ · Structure of PfCSP peptide 21 with antibody iGL-CIS43.D3 · 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 7RAJ · PDBe 7RAJ
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