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Crystal structure of 663 Fab bound to circumsporozoite protein nanp 5- mer

Analyse Crystal structure of 663 Fab bound to circumsporozoite protein nanp 5- mer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BK0
Type: protein
Length: 881 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 663 antibody, light chain; 663 antibody, heavy chain; Circumsporozoite protein nanp 5-mer
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 5 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	663 antibody, light chain	protein	217	6% helix, 52% strand	—
B	663 antibody, heavy chain	protein	222	9% helix, 54% strand	—
C	663 antibody, light chain	protein	214	6% helix, 51% strand	—
D	663 antibody, heavy chain	protein	221	7% helix, 51% strand	—
E	Circumsporozoite protein nanp 5-mer	protein	7	0% helix, 14% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains B, D

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

Pockets

13 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	68	0.75	0.98	18	empty
2	395	0.56	0.74	51	empty
3	51	0.56	0.91	15	empty
4	293	0.53	0.74	43	empty
5	68	0.50	0.85	22	empty

Interfaces

5 interfaces between chains.

A–B · 1763 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1753 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 603 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 300 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 233 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5BK0 · Crystal structure of 663 Fab bound to circumsporozoite protein NANP 5-mer · 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 5BK0 · PDBe 5BK0

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