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Structure of D19.PA8 Fab in complex with 1FD6 16055 V1V2 scaffold

Analyse Structure of D19.PA8 Fab in complex with 1FD6 16055 V1V2 scaffold in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WAS
Type: protein
Length: 967 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GN1_PA8 Fab heavy chain; GN1_PA8 Fab light chain; 1FD6 16055 V1V2 scaffold
Ligands: NAG
Pockets: 9 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	GN1_PA8 Fab heavy chain	protein	219	10% helix, 50% strand	—
L, B	GN1_PA8 Fab light chain	protein	215	9% helix, 49% strand	—
A	GN1_PA8 Fab heavy chain	protein	219	7% helix, 51% strand	—
G	1FD6 16055 V1V2 scaffold	protein	51	6% helix, 43% strand	—
J	1FD6 16055 V1V2 scaffold	protein	48	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G, B, L, J

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

Pockets

9 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	757	0.68	0.76	68	empty
2	405	0.58	0.75	52	empty
3	96	0.47	0.81	21	empty
4	51	0.40	0.82	18	empty
5	51	0.40	0.82	17	empty

Interfaces

7 interfaces between chains.

A–B · 1843 Å² buried · 16 hydrogen bonds · protein-protein
H–L · 1800 Å² buried · 15 hydrogen bonds · protein-protein
L–A · 470 Å² buried · 11 hydrogen bonds · protein-protein
B–G · 425 Å² buried · 9 hydrogen bonds · protein-protein
L–J · 407 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 modified, 3 glycan (disulfide, cyclization, N-glycosylation).

Compared structures

6WAS · Structure of D19.PA8 Fab in complex with 1FD6 16055 V1V2 scaffold · 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 6WAS · PDBe 6WAS

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