MolNFT v1 · #186414 · protein

Crystal structure of pfcsp peptide 21 with vaccine-elicited human anti-malaria antibody M43.149

7RD4 · Antibody M43.149 heavy chain: “Crystal structure of pfcsp peptide 21 with vaccine-elicited human anti-malaria antibody M43.149”. X-ray diffraction, 7 pockets (best druggability 0.83). MolNFT v1 #186414 on GenesisL1: 3D structure…

PDB: 7RD4
Type: protein
Length: 902 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody M43.149 heavy chain; Antibody M43.149 light chain; Circumsporozoite protein
UniProt: P02893
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	Antibody M43.149 heavy chain	protein	220	8% helix, 55% strand	—
L, B	Antibody M43.149 light chain	protein	217	6% helix, 53% strand	—
G	Circumsporozoite protein	protein	15	0% helix, 7% strand	P02893
I	Circumsporozoite protein	protein	13	0% helix, 8% strand	P02893

Pockets

7 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	953	0.83	0.85	104	empty
2	236	0.51	0.75	42	empty
3	61	0.48	0.84	17	empty
4	51	0.43	0.84	22	empty
5	120	0.36	0.73	22	empty

Interfaces

9 interfaces between chains.

A–B · 1927 Å² buried · 19 hydrogen bonds · protein-protein
H–L · 1919 Å² buried · 21 hydrogen bonds · protein-protein
L–G · 474 Å² buried · 4 hydrogen bonds · protein-protein
H–G · 434 Å² buried · 13 hydrogen bonds · protein-protein
B–I · 417 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7RD4 · Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody… · the same entry in another collection · chain I against I, TM-score 1.00
P02893 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P02893) · a predicted model of the same protein · chain I against A, TM-score 0.31

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 P02893
Elsewhere: RCSB PDB 7RD4 · PDBe 7RD4 · UniProt P02893

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