Research workbench

MAGI1_2 complexed with a 16E6 peptide

Analyse MAGI1_2 complexed with a 16E6 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TWQ
Type: protein
Length: 857 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 1,ANNEXIN A2…
UniProt: H7C535, P07355
Ligands: CA
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 1,ANNEXIN A2	protein	422	57% helix, 9% strand	H7C535, P07355
C, D	Thr-arg-arg-glu-thr-gln-leu	protein	7	0% helix, 43% strand	—
A	Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 1,ANNEXIN A2	protein	421	56% helix, 9% strand	H7C535, P07355

Ligands and binding sites

CA · Calcium ion · metal · 11 copies · chains B, A
CIT · Citric acid · additive · 3 copies · chains B, A
GOL · Glycerol · additive · 2 copies · chains B, A

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	509	0.77	0.85	64	GOL
2	705	0.71	0.78	89	GOL
3	306	0.70	0.84	47	empty
4	135	0.56	0.82	28	empty
5	74	0.34	0.76	17	empty

Interfaces

3 interfaces between chains.

D–A · 614 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 540 Å² buried · 9 hydrogen bonds · protein-protein
B–A · 353 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6TWQ · MAGI1_2 complexed with a 16E6 peptide · the same entry in another collection · chain B against B, TM-score 1.00
P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain B against A, TM-score 0.76

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 H7C535
Every structure of UniProt P07355
Elsewhere: RCSB PDB 6TWQ · PDBe 6TWQ · UniProt H7C535 · UniProt P07355

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