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Crystal structure of the third PDZ domain of psd-95 protein: space group P3112

Analyse Crystal structure of the third PDZ domain of psd-95 protein: space group P3112 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QJI
Type: protein
Length: 555 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Disks large homolog 4
UniProt: P78352
Ligands: SO4
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 6 distinct chains · 22% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Disks large homolog 4	protein	90	21% helix, 39% strand	P78352
B	Disks large homolog 4	protein	93	23% helix, 40% strand	P78352
C	Disks large homolog 4	protein	92	21% helix, 42% strand	P78352
D	Disks large homolog 4	protein	91	22% helix, 38% strand	P78352
E	Disks large homolog 4	protein	95	22% helix, 37% strand	P78352
F	Disks large homolog 4	protein	94	22% helix, 37% strand	P78352

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F

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

Pockets

7 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	419	0.65	0.79	45	SO4
2	97	0.43	0.79	18	empty
3	105	0.41	0.77	25	empty
4	161	0.39	0.72	27	empty
5	52	0.34	0.79	18	empty

Interfaces

8 interfaces between chains.

A–B · 619 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 576 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 474 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 351 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 311 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6QJI · Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 · the same entry in another collection · chain F against F, TM-score 1.00
P78352 · AlphaFold monomer V2.0 prediction for disks large homolog 4 (P78352) · a predicted model of the same protein · chain C 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 P78352
Elsewhere: RCSB PDB 6QJI · PDBe 6QJI · UniProt P78352

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