MolNFT v1 · #163524 · protein

Strictosidine synthase from ophiorrhiza pumila in complex with (S)-1- N-propyl-2,3,4,9-tetrahydro-1H-beta-carboline

6S5M: “Strictosidine synthase from ophiorrhiza pumila in complex with (S)-1…”. X-ray diffraction, 1 ligand (KWH), 4 pockets (best druggability 0.63). MolNFT v1 #163524 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6S5M
Type: protein
Length: 306 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Strictosidine synthase
UniProt: Q94LW9
Ligands: KWH
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Strictosidine synthase	protein	306	7% helix, 49% strand	Q94LW9

Ligands and binding sites

KWH · (1~{S})-1-propyl-2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole · ligand · chains A

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	197	0.63	0.83	26	KWH
2	206	0.62	0.82	22	empty
3	52	0.33	0.78	15	empty
4	72	0.31	0.74	14	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6S5M · Strictosidine Synthase from Ophiorrhiza pumila in complex with… · 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 Q94LW9
Elsewhere: RCSB PDB 6S5M · PDBe 6S5M · UniProt Q94LW9

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