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Structure of tetrameric siga complex (class 2)

Analyse Structure of tetrameric siga complex (class 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UE9
Type: protein
Length: 2,475 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 · 6% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Immunoglobulin heavy constant alpha 2	protein	221	9% helix, 41% strand	P01877
B, F, G	Immunoglobulin heavy constant alpha 2	protein	231	10% helix, 42% strand	P01877
C	Polymeric immunoglobulin receptor	protein	537	4% helix, 37% strand	P01833
D	Immunoglobulin J chain	protein	132	3% helix, 35% strand	P01591
E	Immunoglobulin heavy constant alpha 2	protein	227	5% helix, 30% strand	P01877
H	Immunoglobulin heavy constant alpha 2	protein	224	8% helix, 35% strand	P01877
K	Immunoglobulin heavy constant alpha 2	protein	221	10% helix, 38% strand	P01877
L	Immunoglobulin heavy constant alpha 2	protein	220	4% helix, 23% strand	P01877

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	785	0.87	0.90	94	empty
2	1199	0.82	0.83	130	empty
3	76	0.73	0.96	24	empty
4	909	0.72	0.76	91	empty
5	123	0.70	0.91	28	empty

Interfaces

27 interfaces between chains.

F–G · 1920 Å² buried · 15 hydrogen bonds · protein-protein
D–F · 1884 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1838 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1739 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 1666 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 37 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

6UE9 · Structure of tetrameric sIgA complex (Class 2) · 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 6UE9 · PDBe 6UE9 · UniProt P01877 · UniProt P01833 · UniProt P01591

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