MolNFT v1 · #162860 · protein

Crystal structure of the PDZ tandem of syntenin in complex with fragment F13

6RLC · Syntenin-1: “Crystal structure of the PDZ tandem of syntenin in complex with fragment F13”. X-ray diffraction, 1 ligand (K7Z), 8 pockets (best druggability 0.61). MolNFT v1 #162860 on GenesisL1: 3D structure, binding sites and…

PDB: 6RLC
Type: protein
Length: 651 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Syntenin-1
UniProt: O00560
Ligands: K7Z
Pockets: 8 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Syntenin-1	protein	163	17% helix, 39% strand	O00560
B	Syntenin-1	protein	162	17% helix, 40% strand	O00560
D	Syntenin-1	protein	163	17% helix, 39% strand	O00560

Ligands and binding sites

K7Z · (2~{S})-2-[3-(4-chlorophenyl)sulfanylpropanoylamino]-3-methyl-butanoic acid · ligand · 4 copies · chains A, B, C, D
ACT · Acetate ion · additive · 3 copies · chains A, B, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	272	0.61	0.79	42	empty
2	236	0.56	0.77	36	empty
3	242	0.55	0.77	32	K7Z
4	59	0.35	0.77	12	K7Z
5	79	0.34	0.75	16	empty

Interfaces

3 interfaces between chains.

C–D · 1067 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1058 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 204 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6RLC · Crystal structure of the PDZ tandem of syntenin in complex with fragment F13 · the same entry in another collection · chain A against A, TM-score 1.00

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 O00560
Elsewhere: RCSB PDB 6RLC · PDBe 6RLC · UniProt O00560

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