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Crystal structure of IG1 domain of mouse syncam 2

Analyse Crystal structure of IG1 domain of mouse syncam 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M45
Type: protein
Length: 396 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell adhesion molecule 2
UniProt: Q8BLQ9
Ligands: NAG
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cell adhesion molecule 2	protein	101	3% helix, 51% strand	Q8BLQ9
C	Cell adhesion molecule 2	protein	97	3% helix, 49% strand	Q8BLQ9
D	Cell adhesion molecule 2	protein	97	3% helix, 54% strand	Q8BLQ9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, D, B, C

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	56	0.38	0.80	15	empty
2	50	0.23	0.72	12	empty

Interfaces

3 interfaces between chains.

B–C · 723 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 701 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 311 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

3M45 · Crystal structure of Ig1 domain of mouse SynCAM 2 · the same entry in another collection · chain D against D, TM-score 1.00
Q8BLQ9 · AlphaFold monomer V2.0 prediction for cell adhesion molecule 2 (Q8BLQ9) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q8BLQ9
Elsewhere: RCSB PDB 3M45 · PDBe 3M45 · UniProt Q8BLQ9

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