MolNFT v1 · #142927 · protein

Crystal structure of the syntenin PDZ1 domain in complex with the peptide inhibitor ksl-128018

6AK2 · Syntenin-1: “Crystal structure of the syntenin PDZ1 domain in complex with the peptide inhibitor ksl-128018”. X-ray diffraction. MolNFT v1 #142927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6AK2
Type: protein
Length: 173 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Syntenin-1; Peptide inhibitor ksl-128018
UniProt: Q9JI92

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Syntenin-1	protein	78	15% helix, 38% strand	Q9JI92
B	Syntenin-1	protein	81	17% helix, 40% strand	Q9JI92
D, E	Peptide inhibitor ksl-128018	protein	7	0% helix, 43% strand	—

Interfaces

3 interfaces between chains.

B–E · 664 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 625 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 495 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

6AK2 · Crystal structure of the syntenin PDZ1 domain in complex with the peptide inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
Q9JI92 · AlphaFold monomer V2.0 prediction for syntenin-1 (Q9JI92) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 Q9JI92
Elsewhere: RCSB PDB 6AK2 · PDBe 6AK2 · UniProt Q9JI92

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