MolNFT v1 · #151333 · protein

Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal peptide

6HKS · Tyrosine-protein phosphatase non-receptor type 3: “Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal peptide”. X-ray diffraction, 1 ligand (IOD), 7 pockets (best druggability 0.57). MolNFT v1…

PDB: 6HKS
Type: protein
Length: 594 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein phosphatase non-receptor type 3; Protein E6
EC: 3.1.3.48
UniProt: P26045, P03126
Ligands: IOD
Pockets: 7 · best druggability 0.57

Structure

x-ray diffraction · 6 distinct chains · 18% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, F	Tyrosine-protein phosphatase non-receptor type 3 (EC 3.1.3.48)	protein	93	15% helix, 38% strand	P26045
B	Tyrosine-protein phosphatase non-receptor type 3 (EC 3.1.3.48)	protein	94	18% helix, 37% strand	P26045
C	Tyrosine-protein phosphatase non-receptor type 3 (EC 3.1.3.48)	protein	91	19% helix, 36% strand	P26045
D	Tyrosine-protein phosphatase non-receptor type 3 (EC 3.1.3.48)	protein	92	22% helix, 36% strand	P26045
G, L	Protein E6	protein	7	0% helix, 43% strand	P03126
H, I, J, K	Protein E6	protein	6	0% helix, 50% strand	P03126

Ligands and binding sites

IOD · Iodide ion · ion · 6 copies · chains A, C, B, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.57	0.81	36	IOD
2	182	0.57	0.81	31	empty
3	123	0.53	0.82	23	empty
4	92	0.48	0.82	22	empty
5	243	0.46	0.73	35	empty

Interfaces

13 interfaces between chains.

F–L · 586 Å² buried · 14 hydrogen bonds · protein-protein
A–G · 572 Å² buried · 15 hydrogen bonds · protein-protein
C–I · 535 Å² buried · 19 hydrogen bonds · protein-protein
B–H · 529 Å² buried · 14 hydrogen bonds · protein-protein
E–K · 524 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6HKS · Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal… · the same entry in another collection · chain L against L, 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 P26045
Every structure of UniProt P03126
Elsewhere: RCSB PDB 6HKS · PDBe 6HKS · UniProt P26045 · UniProt P03126

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