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Sphingomonas wittichii serine palmitoyltransferase

Analyse Sphingomonas wittichii serine palmitoyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X8U
Type: protein
Length: 798 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine palmitoyltransferase
EC: 2.3.1.50
UniProt: A5VD79
Ligands: PLP
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Serine palmitoyltransferase (EC 2.3.1.50)	protein	399	42% helix, 19% strand	A5VD79

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B

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

Pockets

8 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	801	0.80	0.83	79	PLP
2	763	0.80	0.83	78	PLP
3	138	0.46	0.77	28	empty
4	123	0.45	0.78	27	empty
5	68	0.40	0.80	17	empty

Interfaces

1 interface between chains.

A–B · 3799 Å² buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

2X8U · Sphingomonas wittichii Serine palmitoyltransferase · 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 A5VD79
Elsewhere: RCSB PDB 2X8U · PDBe 2X8U · UniProt A5VD79

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