MolNFT v1 · #158648 · protein

SAXIPHILIN:STX complex, soaking

6O0E: “SAXIPHILIN:STX complex, soaking”. X-ray diffraction, 1 ligand (9SL), 20 pockets (best druggability 0.78). MolNFT v1 #158648 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6O0E
Type: protein
Length: 1,614 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Saxiphilin
UniProt: P31226
Ligands: 9SL
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Saxiphilin	protein	799	28% helix, 17% strand	P31226
B	Saxiphilin	protein	815	27% helix, 18% strand	P31226

Ligands and binding sites

9SL · [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate · ligand · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1143	0.78	0.80	128	empty
2	782	0.76	0.81	81	empty
3	882	0.70	0.76	74	empty
4	171	0.70	0.89	34	empty
5	171	0.69	0.88	32	empty

Interfaces

1 interface between chains.

A–B · 301 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

6O0E · Saxiphilin:STX complex, soaking · the same entry in another collection · chain A against A, TM-score 1.00
P31226 · AlphaFold monomer V2.0 prediction for saxiphilin (P31226) · a predicted model of the same protein · chain B against A, TM-score 0.76

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 P31226
Elsewhere: RCSB PDB 6O0E · PDBe 6O0E · UniProt P31226

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