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Crystal structure of FAB395 in complex with NPNA2 peptide from circumsporozoite protein

Analyse Crystal structure of FAB395 in complex with NPNA2 peptide from circumsporozoite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WFX
Type: protein
Length: 440 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAB395 heavy chain; FAB395 light chain; NPNA2 peptide
Ligands: ACE
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	FAB395 heavy chain	protein	224	7% helix, 48% strand	—
L	FAB395 light chain	protein	210	6% helix, 51% strand	—
P	NPNA2 peptide	protein	6	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains H, P

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	139	0.44	0.76	22	empty
2	172	0.43	0.74	26	empty
3	54	0.25	0.72	12	empty

Interfaces

3 interfaces between chains.

H–L · 1873 Å² buried · 15 hydrogen bonds · protein-protein
H–P · 417 Å² buried · 10 hydrogen bonds · protein-protein
L–P · 36 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

6WFX · Crystal structure of Fab395 in complex with NPNA2 peptide from circumsporozoite protein · the same entry in another collection · chain H against H, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6WFX · PDBe 6WFX

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