MolNFT v1 · #70553 · protein

Second PDZ domain from human PTP1E

3LNX · Tyrosine-protein phosphatase non-receptor type 13: “Second PDZ domain from human PTP1E”. X-ray diffraction, 2 ligands (IOD, SCN), 10 pockets (best druggability 0.86). MolNFT v1 #70553 on GenesisL1: 3D structure, binding sites and…

PDB: 3LNX
Type: protein
Length: 564 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein phosphatase non-receptor type 13
UniProt: Q12923
Ligands: IOD, SCN
Pockets: 10 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Tyrosine-protein phosphatase non-receptor type 13	protein	94	18% helix, 37% strand	Q12923

Ligands and binding sites

IOD · Iodide ion · ion · 25 copies · chains A, E, F, C, B, D
SCN · Thiocyanate ion · ion · 14 copies · chains A, B, C, E, D, F

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1002	0.86	0.87	97	IOD, SCN
2	94	0.73	0.95	30	SCN
3	89	0.72	0.95	30	empty
4	101	0.72	0.94	31	SCN
5	70	0.38	0.78	13	IOD, SCN

Interfaces

12 interfaces between chains.

A–B · 720 Å² buried · 15 hydrogen bonds · protein-protein
D–F · 711 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 689 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 307 Å² buried · 1 hydrogen bond · protein-protein
C–D · 300 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3LNX · Second PDZ domain from human PTP1E · the same entry in another collection · chain C against C, TM-score 1.00
Q12923 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 13… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q12923
Elsewhere: RCSB PDB 3LNX · PDBe 3LNX · UniProt Q12923

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