Research workbench

Structure of chimeric antibody F10HEAVY_L9LIGHT with pfcsp peptide nanpnvdp

Analyse Structure of chimeric antibody F10HEAVY_L9LIGHT with pfcsp peptide nanpnvdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RQQ
Type: protein
Length: 437 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: F10 heavy chain; L9 kappa chain; Pfcsp peptide nanpnvdp
Ligands: SO4
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	F10 heavy chain	protein	219	7% helix, 57% strand	—
L	L9 kappa chain	protein	212	6% helix, 52% strand	—
P	Pfcsp peptide nanpnvdp	protein	6	0% helix, 17% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains H
EDO · 1,2-ethanediol · additive · 3 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	654	0.65	0.75	67	EDO
2	69	0.52	0.86	23	empty
3	185	0.44	0.74	33	empty
4	76	0.35	0.76	23	empty

Interfaces

3 interfaces between chains.

H–L · 1895 Å² buried · 16 hydrogen bonds · protein-protein
H–P · 228 Å² buried · 3 hydrogen bonds · protein-protein
L–P · 219 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).

Compared structures

7RQQ · Structure of chimeric antibody F10heavy_L9light with PfCSP peptide NANPNVDP · 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 7RQQ · PDBe 7RQQ

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