MolNFT v1 · #136875 · protein

Crystal structure of myosin VI in complex with GH2 domain of GIPC2

5V6H · PDZ domain-containing protein GIPC2: “Crystal structure of myosin VI in complex with GH2 domain of GIPC2”. X-ray diffraction, 9 pockets (best druggability 0.53). MolNFT v1 #136875 on GenesisL1: 3D structure, binding sites and…

PDB: 5V6H
Type: protein
Length: 591 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PDZ domain-containing protein GIPC2; Unconventional myosin-VI
UniProt: Q9Z2H7, Q64331
Pockets: 9 · best druggability 0.53

Structure

x-ray diffraction · 5 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PDZ domain-containing protein GIPC2	protein	75	73% helix, 0% strand	Q9Z2H7
B, D, F, J	Unconventional myosin-VI	protein	44	73% helix, 0% strand	Q64331
C, G, I	PDZ domain-containing protein GIPC2	protein	73	66% helix, 0% strand	Q9Z2H7
E	PDZ domain-containing protein GIPC2	protein	76	63% helix, 0% strand	Q9Z2H7
H	Unconventional myosin-VI	protein	45	80% helix, 0% strand	Q64331

Pockets

9 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	210	0.53	0.77	26	empty
2	139	0.46	0.77	23	empty
3	112	0.40	0.76	18	empty
4	61	0.37	0.79	17	empty
5	72	0.37	0.77	15	empty

Interfaces

13 interfaces between chains.

C–D · 742 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 728 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 722 Å² buried · 4 hydrogen bonds · protein-protein
I–J · 586 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 577 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5V6H · Crystal structure of Myosin VI in complex with GH2 domain of GIPC2 · the same entry in another collection · chain J against J, TM-score 1.00
Q9Z2H7 · AlphaFold monomer V2.0 prediction for PDZ domain-containing protein GIPC2 (Q9Z2H7) · a predicted model of the same protein · chain C 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 Q9Z2H7
Every structure of UniProt Q64331
Elsewhere: RCSB PDB 5V6H · PDBe 5V6H · UniProt Q9Z2H7 · UniProt Q64331

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