MolNFT v1 · #11844 · protein

Structure of the salmonella virulence effector sptp in complex with its secretion chaperone sicp

1JYO: “Structure of the salmonella virulence effector sptp in complex with its secretion chaperone sicp”. X-ray diffraction, 9 pockets (best druggability 0.61). MolNFT v1 #11844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JYO
Type: protein
Length: 726 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sicp; Protein tyrosine phosphatase sptp
UniProt: O85300, P74873
Pockets: 9 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Sicp	protein	130	45% helix, 28% strand	O85300
E	Protein tyrosine phosphatase sptp	protein	102	51% helix, 12% strand	P74873
F	Protein tyrosine phosphatase sptp	protein	104	48% helix, 10% strand	P74873

Pockets

9 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	285	0.61	0.79	37	empty
2	243	0.60	0.80	32	empty
3	202	0.56	0.79	39	empty
4	202	0.49	0.76	35	empty
5	116	0.45	0.78	24	empty

Interfaces

9 interfaces between chains.

D–E · 1627 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 1616 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1180 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 1170 Å² buried · 15 hydrogen bonds · protein-protein
A–F · 1120 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

1JYO · Structure of the Salmonella Virulence Effector SptP in Complex with its Secretion… · the same entry in another collection · chain F against F, TM-score 1.00
P74873 · AlphaFold monomer V2.0 prediction for secreted effector protein sptp (P74873) · a predicted model of the same protein · chain F against A, TM-score 0.41

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 O85300
Every structure of UniProt P74873
Elsewhere: RCSB PDB 1JYO · PDBe 1JYO · UniProt O85300 · UniProt P74873

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