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Crystal structure of malaria transmission-blocking antigen PFS48/45 6C in complex with antibody 85RF45.1

Analyse Crystal structure of malaria transmission-blocking antigen PFS48/45 6C in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6E62
Type: protein
Length: 1,134 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PF48/45; 85RF45.1 Fab heavy chain; 85RF45.1 Fab light chain
UniProt: A8QVT1
Ligands: NAG
Pockets: 12 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P, A	PF48/45	protein	137	6% helix, 50% strand	A8QVT1
H, B	85RF45.1 Fab heavy chain	protein	217	6% helix, 57% strand	—
L, C	85RF45.1 Fab light chain	protein	213	6% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains P, A
GOL · Glycerol · additive · 2 copies · chains P, H, A, B

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	474	0.62	0.76	60	empty
2	224	0.52	0.77	33	empty
3	249	0.51	0.75	29	empty
4	156	0.50	0.78	23	empty
5	85	0.47	0.82	16	empty

Interfaces

10 interfaces between chains.

H–L · 1943 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1912 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 744 Å² buried · 15 hydrogen bonds · protein-protein
P–H · 730 Å² buried · 13 hydrogen bonds · protein-protein
P–L · 449 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6E62 · Crystal structure of malaria transmission-blocking antigen Pfs48/45 6C in complex with… · the same entry in another collection · chain P against P, 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 A8QVT1
Elsewhere: RCSB PDB 6E62 · PDBe 6E62 · UniProt A8QVT1

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