Research workbench

Structure of chimeric antibody L9HEAVY_F10LIGHT with pfcsp peptide nanpnvdp

Analyse Structure of chimeric antibody L9HEAVY_F10LIGHT 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: 7RQR
Type: protein
Length: 873 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L9 heavy chain; F10 kappa chain; Pfcsp peptide nanpnvdp
Pockets: 11 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L9 heavy chain	protein	215	6% helix, 54% strand	—
B, L	F10 kappa chain	protein	213	6% helix, 51% strand	—
C, P	Pfcsp peptide nanpnvdp	protein	6	0% helix, 17% strand	—
H	L9 heavy chain	protein	220	4% helix, 52% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains A, C

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

Pockets

11 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	788	0.67	0.75	67	empty
2	682	0.65	0.74	61	empty
3	258	0.64	0.82	45	empty
4	61	0.55	0.89	21	empty
5	52	0.48	0.87	20	empty

Interfaces

7 interfaces between chains.

H–L · 1927 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1773 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 363 Å² buried · 5 hydrogen bonds · protein-protein
H–P · 228 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 225 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).

Compared structures

7RQR · Structure of chimeric antibody L9heavy_F10light with PfCSP peptide NANPNVDP · the same entry in another collection · chain A against A, 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 7RQR · PDBe 7RQR

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