Research workbench

Fab fragment complexed with C-mannosylated tryptophan peptide

Analyse Fab fragment complexed with C-mannosylated tryptophan peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PLH
Type: protein
Length: 446 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 5G12 light chain; Fab 5G12 heavy chain; Interleukin-21 receptor
UniProt: Q9HBE5
Ligands: MAN, PO4
Pockets: 6 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab 5G12 light chain	protein	219	5% helix, 52% strand	—
B	Fab 5G12 heavy chain	protein	219	7% helix, 51% strand	—
C	Interleukin-21 receptor	protein	8	0% helix, 13% strand	Q9HBE5

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · chains A, B, C
PO4 · Phosphate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	252	0.50	0.75	34	empty
2	142	0.44	0.76	28	empty
3	124	0.41	0.75	26	empty
4	123	0.39	0.74	21	empty
5	63	0.36	0.78	17	MAN

Interfaces

3 interfaces between chains.

A–B · 1875 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 313 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 121 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 glycan, 1 modified (disulfide, C-mannosylation, cyclization).

Compared structures

6PLH · FAB fragment complexed with C-mannosylated tryptophan peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q9HBE5 · AlphaFold monomer V2.0 prediction for interleukin-21 receptor (Q9HBE5) · a predicted model of the same protein · chain C against A, TM-score 0.59

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 Q9HBE5
Elsewhere: RCSB PDB 6PLH · PDBe 6PLH · UniProt Q9HBE5

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