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Crystal structure of FAB239 in complex with NPNA4 peptide from circumsporozoite protein

Analyse Crystal structure of FAB239 in complex with NPNA4 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: 6WG2
Type: protein
Length: 878 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAB239 heavy chain; FAB239 light chain; NPNA4 peptide
Ligands: ACE
Pockets: 7 · best druggability 0.55

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	FAB239 heavy chain	protein	217	6% helix, 52% strand	—
I	FAB239 heavy chain	protein	216	7% helix, 52% strand	—
L	FAB239 light chain	protein	214	5% helix, 50% strand	—
M	FAB239 light chain	protein	215	6% helix, 51% strand	—
P	NPNA4 peptide	protein	16	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains H, L, P

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

Pockets

7 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	287	0.55	0.76	33	empty
2	312	0.53	0.74	38	empty
3	300	0.52	0.74	41	empty
4	156	0.43	0.75	33	empty
5	95	0.35	0.74	23	empty

Interfaces

10 interfaces between chains.

H–L · 1743 Å² buried · 15 hydrogen bonds · protein-protein
I–M · 1709 Å² buried · 13 hydrogen bonds · protein-protein
I–P · 480 Å² buried · 7 hydrogen bonds · protein-protein
H–P · 458 Å² buried · 5 hydrogen bonds · protein-protein
H–I · 387 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

6WG2 · Crystal structure of Fab239 in complex with NPNA4 peptide from circumsporozoite protein · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 6WG2 · PDBe 6WG2

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