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Crystal structure of the zig-8 IG1 homodimer

Analyse Crystal structure of the zig-8 IG1 homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PLL
Type: protein
Length: 349 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Zwei ig domain protein zig-8
UniProt: G5ED00
Ligands: NAG, SO4
Pockets: 4 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Zwei ig domain protein zig-8	protein	118	11% helix, 44% strand	G5ED00
B	Zwei ig domain protein zig-8	protein	116	12% helix, 45% strand	G5ED00
C	Zwei ig domain protein zig-8	protein	115	8% helix, 43% strand	G5ED00

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

4 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	209	0.54	0.78	31	empty
2	168	0.44	0.75	25	SO4
3	52	0.34	0.79	16	empty
4	52	0.30	0.77	12	empty

Interfaces

3 interfaces between chains.

A–B · 865 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 570 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 142 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6PLL · Crystal structure of the ZIG-8 IG1 homodimer · the same entry in another collection · chain A against A, TM-score 1.00
G5ED00 · AlphaFold monomer V2.0 prediction for zwei ig domain protein zig-8 (G5ED00) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 G5ED00
Elsewhere: RCSB PDB 6PLL · PDBe 6PLL · UniProt G5ED00

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