MolNFT v1 · #185183 · protein

Pfcyrpa bound to monoclonal antibody CY.002 Fab fragment

7PI7 · Cysteine-rich protective antigen: “Pfcyrpa bound to monoclonal antibody CY.002 Fab fragment”. X-ray diffraction, 17 pockets (best druggability 0.83). MolNFT v1 #185183 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7PI7
Type: protein
Length: 1,501 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cysteine-rich protective antigen; Monoclonal antibody CY.002 heavy chain; Monoclonal…
UniProt: Q8IFM8
Pockets: 17 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 3% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cysteine-rich protective antigen	protein	317	0% helix, 59% strand	Q8IFM8
B	Monoclonal antibody CY.002 heavy chain	protein	216	4% helix, 47% strand	—
C, F	Monoclonal antibody CY.002 light chain	protein	216	6% helix, 54% strand	—
D	Cysteine-rich protective antigen	protein	317	1% helix, 56% strand	Q8IFM8
E	Monoclonal antibody CY.002 heavy chain	protein	219	4% helix, 48% strand	—

Pockets

17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	644	0.83	0.87	72	empty
2	619	0.83	0.88	83	empty
3	849	0.69	0.75	71	empty
4	733	0.68	0.76	56	empty
5	138	0.46	0.77	25	empty

Interfaces

8 interfaces between chains.

B–C · 1916 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1893 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 838 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 837 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 532 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

7PI7 · PfCyRPA bound to monoclonal antibody Cy.002 Fab fragment · the same entry in another collection · chain F against F, TM-score 1.00
Q8IFM8 · AlphaFold monomer V2.0 prediction for cysteine-rich protective antigen (Q8IFM8) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q8IFM8
Elsewhere: RCSB PDB 7PI7 · PDBe 7PI7 · UniProt Q8IFM8

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