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Crystal structure of FAB239 in complex with NPNA2 peptide from circumsporozoite protein

Analyse Crystal structure of FAB239 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: 6W00
Type: protein
Length: 505 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin G-binding protein G; FAB239 light chain; FAB239 heavy chain; NPNA2 peptide
UniProt: P19909
Ligands: ACE
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Immunoglobulin G-binding protein G	protein	58	24% helix, 47% strand	P19909
L	FAB239 light chain	protein	215	7% helix, 50% strand	—
H	FAB239 heavy chain	protein	224	8% helix, 50% strand	—
P	NPNA2 peptide	protein	8	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains L, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	361	0.54	0.74	51	empty
2	143	0.52	0.80	30	empty
3	68	0.32	0.75	16	empty

Interfaces

5 interfaces between chains.

L–H · 2032 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 572 Å² buried · 13 hydrogen bonds · protein-protein
H–P · 461 Å² buried · 5 hydrogen bonds · protein-protein
L–P · 205 Å² buried · 3 hydrogen bonds · protein-protein
G–L · 168 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

6W00 · Crystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein · the same entry in another collection · chain L against L, 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
Every structure of UniProt P19909
Elsewhere: RCSB PDB 6W00 · PDBe 6W00 · UniProt P19909

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