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Structure of tetrameric siga complex (class 1)

Analyse Structure of tetrameric siga complex (class 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UE8
Type: protein
Length: 2,473 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin heavy constant alpha 2; Polymeric immunoglobulin receptor; Immunoglobulin…
UniProt: P01877, P01833, P01591
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 8 distinct chains · 7% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Immunoglobulin heavy constant alpha 2	protein	221	8% helix, 39% strand	P01877
B, F, G	Immunoglobulin heavy constant alpha 2	protein	231	9% helix, 38% strand	P01877
C	Polymeric immunoglobulin receptor	protein	535	4% helix, 36% strand	P01833
D	Immunoglobulin J chain	protein	132	3% helix, 38% strand	P01591
E	Immunoglobulin heavy constant alpha 2	protein	227	7% helix, 29% strand	P01877
H	Immunoglobulin heavy constant alpha 2	protein	224	11% helix, 38% strand	P01877
K	Immunoglobulin heavy constant alpha 2	protein	221	10% helix, 38% strand	P01877
L	Immunoglobulin heavy constant alpha 2	protein	220	5% helix, 21% strand	P01877

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains C, D, A, B, F, G
BMA · beta-D-mannopyranose · sugar

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1163	0.87	0.88	116	empty
2	1068	0.81	0.82	93	empty
3	117	0.74	0.93	31	empty
4	939	0.71	0.76	102	empty
5	539	0.70	0.79	68	empty

Interfaces

30 interfaces between chains.

D–F · 1957 Å² buried · 30 hydrogen bonds · protein-protein
F–G · 1900 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1846 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1751 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 1619 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 37 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

6UE8 · Structure of tetrameric sIgA complex (Class 1) · the same entry in another collection · chain L against L, TM-score 1.00
P01833 · AlphaFold monomer V2.0 prediction for polymeric immunoglobulin receptor (P01833) · a predicted model of the same protein · chain C against A, TM-score 0.95
P01591 · AlphaFold monomer V2.0 prediction for immunoglobulin J chain (P01591) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 P01877
Every structure of UniProt P01833
Every structure of UniProt P01591
Elsewhere: RCSB PDB 6UE8 · PDBe 6UE8 · UniProt P01877 · UniProt P01833 · UniProt P01591

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