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Pfcyrpa bound to Fab fragments from monoclonal antibodies CY.003, CY.004 and CY.007

Analyse Pfcyrpa bound to Fab fragments from monoclonal antibodies CY.003, CY.004 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PI3
Type: protein
Length: 6,419 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cysteine-rich protective antigen; Monoclonal antibody CY.003 heavy chain; Monoclonal…
UniProt: Q8IFM8
Ligands: CA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 20 distinct chains · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cysteine-rich protective antigen	protein	328	1% helix, 53% strand	Q8IFM8
B, I, P	Monoclonal antibody CY.003 heavy chain	protein	221	6% helix, 47% strand	—
C, J, Q	Monoclonal antibody CY.003 light chain	protein	207	8% helix, 51% strand	—
D, R, Y	Monoclonal antibody CY.007 heavy chain	protein	221	5% helix, 48% strand	—
E	Monoclonal antibody CY.007 light chain	protein	204	5% helix, 46% strand	—
F, M	Monoclonal antibody CY.004 heavy chain	protein	223	4% helix, 50% strand	—
G, N	Monoclonal antibody CY.004 light chain	protein	209	6% helix, 46% strand	—
H	Cysteine-rich protective antigen	protein	321	1% helix, 56% strand	Q8IFM8
K	Monoclonal antibody CY.007 heavy chain	protein	220	5% helix, 48% strand	—
L	Monoclonal antibody CY.007 light chain	protein	203	5% helix, 51% strand	—
O	Cysteine-rich protective antigen	protein	327	2% helix, 54% strand	Q8IFM8
S	Monoclonal antibody CY.007 light chain	protein	200	7% helix, 45% strand	—
T	Monoclonal antibody CY.004 heavy chain	protein	218	5% helix, 50% strand	—
U	Monoclonal antibody CY.004 light chain	protein	208	6% helix, 45% strand	—
V	Cysteine-rich protective antigen	protein	325	1% helix, 57% strand	Q8IFM8
W	Monoclonal antibody CY.003 heavy chain	protein	218	4% helix, 42% strand	—
X	Monoclonal antibody CY.003 light chain	protein	206	8% helix, 50% strand	—
Z	Monoclonal antibody CY.007 light chain	protein	203	5% helix, 43% strand	—
a	Monoclonal antibody CY.004 heavy chain	protein	219	5% helix, 52% strand	—
b	Monoclonal antibody CY.004 light chain	protein	208	5% helix, 47% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, F, G, H, M, N, O, T, U, V, a, b

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1092	0.83	0.85	128	CA
2	922	0.83	0.85	111	empty
3	1051	0.83	0.84	118	empty
4	868	0.83	0.85	93	empty
5	633	0.81	0.86	72	empty

Interfaces

76 interfaces between chains.

F–G · 2015 Å² buried · 23 hydrogen bonds · protein-protein
I–J · 1953 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 1907 Å² buried · 27 hydrogen bonds · protein-protein
T–U · 1899 Å² buried · 19 hydrogen bonds · protein-protein
P–Q · 1896 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 76 disulfide (disulfide).

Compared structures

7PI3 · PfCyRPA bound to Fab fragments from monoclonal antibodies Cy.003, Cy.004 and Cy.007 · the same entry in another collection · chain J against J, 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
Every structure of UniProt Q8IFM8
Elsewhere: RCSB PDB 7PI3 · PDBe 7PI3 · UniProt Q8IFM8

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