MolNFT v1 · #103663 · protein

Crystal structure of the [4+2]-cyclase spnf

4PNE · Methyltransferase-like protein: “Crystal structure of the [4+2]-cyclase spnf”. X-ray diffraction, 1 ligand (SAH), 9 pockets (best druggability 0.79). MolNFT v1 #103663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PNE
Type: protein
Length: 542 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyltransferase-like protein
UniProt: Q9ALM7
Ligands: SAH
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyltransferase-like protein	protein	270	44% helix, 21% strand	Q9ALM7
B	Methyltransferase-like protein	protein	272	44% helix, 21% strand	Q9ALM7

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
MLI · Malonate ion · additive · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	323	0.79	0.89	32	MLI
2	386	0.77	0.86	34	MLI
3	113	0.77	0.97	32	SAH
4	128	0.76	0.95	32	SAH
5	219	0.55	0.78	27	empty

Interfaces

1 interface between chains.

A–B · 696 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4PNE · Crystal Structure of the [4+2]-Cyclase SpnF · the same entry in another collection · chain B against B, 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 Q9ALM7
Elsewhere: RCSB PDB 4PNE · PDBe 4PNE · UniProt Q9ALM7

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