MolNFT v1 · #171373 · protein

Structure of plasmodium falciparum P113 bound to antibody P3.2

6Z2L · Surface protein P113: “Structure of plasmodium falciparum P113 bound to antibody P3.2”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.62). MolNFT v1 #171373 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6Z2L
Type: protein
Length: 631 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Surface protein P113; Fab fragment - vl chain; Fab fragment - vh chain
UniProt: Q8ILP3
Ligands: SO4
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Surface protein P113	protein	197	17% helix, 42% strand	Q8ILP3
B	Fab fragment - vl chain	protein	213	7% helix, 51% strand	—
C	Fab fragment - vh chain	protein	221	7% helix, 50% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	633	0.62	0.73	86	empty
2	195	0.45	0.74	29	empty
3	105	0.38	0.75	19	empty
4	55	0.38	0.80	16	empty
5	63	0.31	0.75	22	empty

Interfaces

3 interfaces between chains.

B–C · 1865 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 697 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 253 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 4 modified (disulfide, methylation).

Compared structures

6Z2L · Structure of Plasmodium falciparum P113 bound to antibody P3.2 · the same entry in another collection · chain A against A, TM-score 1.00
Q8ILP3 · AlphaFold monomer V2.0 prediction for surface protein P113 (Q8ILP3) · a predicted model of the same protein · 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
Every structure of UniProt Q8ILP3
Elsewhere: RCSB PDB 6Z2L · PDBe 6Z2L · UniProt Q8ILP3

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