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Crystal structure of psd-95 SH3-gk domain in complex with a synthesized inhibitor

Analyse Crystal structure of psd-95 SH3-gk domain in complex with a synthesized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YPR
Type: protein
Length: 283 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Disks large homolog 4; Synthesized gk inhibitor
UniProt: P31016
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Disks large homolog 4	protein	267	34% helix, 27% strand	P31016
B	Synthesized gk inhibitor	protein	16	44% helix, 13% strand	—

Pockets

3 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	168	0.59	0.82	36	empty
2	198	0.48	0.75	26	empty
3	57	0.31	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 929 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5YPR · Crystal Structure of PSD-95 SH3-GK domain in complex with a synthesized inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P31016 · AlphaFold monomer V2.0 prediction for disks large homolog 4 (P31016) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P31016
Elsewhere: RCSB PDB 5YPR · PDBe 5YPR · UniProt P31016

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