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Structure of phosphoserine (psab) scaffold bound to pser peptide

Analyse Structure of phosphoserine (psab) scaffold bound to pser peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JFZ
Type: protein
Length: 446 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain; Phosphopeptide
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	214	6% helix, 50% strand	—
H	Fab heavy chain	protein	223	7% helix, 52% strand	—
P	Phosphopeptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

PPI · Propanoic acid · additive · chains L

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	249	0.63	0.81	38	empty
2	295	0.51	0.74	43	PPI
3	104	0.35	0.74	24	empty
4	91	0.32	0.73	12	empty

Interfaces

3 interfaces between chains.

L–H · 1842 Å² buried · 15 hydrogen bonds · protein-protein
H–P · 404 Å² buried · 11 hydrogen bonds · protein-protein
L–P · 222 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, phosphorylation).

Compared structures

4JFZ · Structure of phosphoserine (pSAb) scaffold bound to pSer peptide · 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
Elsewhere: RCSB PDB 4JFZ · PDBe 4JFZ

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