MolNFT v1 · #64880 · protein

Crystal structure of the PDZ domain of PDZ domain-containing protein GIPC2

3GGE: “Crystal structure of the PDZ domain of PDZ domain-containing protein GIPC2”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.67). MolNFT v1 #64880 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3GGE
Type: protein
Length: 282 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PDZ domain-containing protein GIPC2
UniProt: Q8TF65
Ligands: SO4
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	PDZ domain-containing protein GIPC2	protein	95	15% helix, 38% strand	Q8TF65
B	PDZ domain-containing protein GIPC2	protein	92	11% helix, 37% strand	Q8TF65

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B, C
GOL · Glycerol · additive · chains 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	476	0.67	0.79	51	SO4
2	116	0.46	0.79	24	GOL

Interfaces

3 interfaces between chains.

A–C · 574 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 498 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 477 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3GGE · Crystal structure of the PDZ domain of PDZ domain-containing protein GIPC2 · the same entry in another collection · chain A against A, TM-score 1.00
Q8TF65 · AlphaFold monomer V2.0 prediction for PDZ domain-containing protein GIPC2 (Q8TF65) · a predicted model of the same protein · chain C against A, TM-score 0.93

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 Q8TF65
Elsewhere: RCSB PDB 3GGE · PDBe 3GGE · UniProt Q8TF65

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