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Structure of secretory IgM core

Analyse Structure of secretory IgM core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K0C
Type: protein
Length: 2,898 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymeric immunoglobulin receptor; Immunoglobulin heavy constant mu; Immunoglobulin J…
UniProt: P01833, P01871, P01591
Ligands: NAG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 9 distinct chains · 8% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Polymeric immunoglobulin receptor	protein	534	7% helix, 41% strand	P01833
A, B	Immunoglobulin heavy constant mu	protein	227	9% helix, 39% strand	P01871
K	Immunoglobulin heavy constant mu	protein	225	8% helix, 39% strand	P01871
L, I, E	Immunoglobulin heavy constant mu	protein	224	10% helix, 33% strand	P01871
J	Immunoglobulin heavy constant mu	protein	221	5% helix, 32% strand	P01871
H	Immunoglobulin heavy constant mu	protein	230	10% helix, 36% strand	P01871
D	Immunoglobulin J chain	protein	104	4% helix, 23% strand	P01591
G	Immunoglobulin heavy constant mu	protein	230	10% helix, 30% strand	P01871
F	Immunoglobulin heavy constant mu	protein	228	6% helix, 32% strand	P01871

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.88	0.90	115	empty
2	1169	0.83	0.84	123	empty
3	1040	0.82	0.83	93	empty
4	90	0.76	0.97	22	empty
5	725	0.72	0.78	61	empty

Interfaces

36 interfaces between chains.

A–B · 1680 Å² buried · 21 hydrogen bonds · protein-protein
G–F · 1593 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 1563 Å² buried · 22 hydrogen bonds · protein-protein
E–H · 1538 Å² buried · 15 hydrogen bonds · protein-protein
K–L · 1490 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7K0C · Structure of Secretory IgM Core · the same entry in another collection · chain F against F, 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
Every structure of UniProt P01833
Every structure of UniProt P01871
Every structure of UniProt P01591
Elsewhere: RCSB PDB 7K0C · PDBe 7K0C · UniProt P01833 · UniProt P01871 · UniProt P01591

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