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Crystal Structure of the SpnL

Analyse Crystal Structure of the SpnL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7V6H
Type: protein
Length: 534 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.054
Source: Saccharopolyspora spinosa
Molecule: Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase
UniProt: A0A2N3Y640
Ligands: SAH
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · resolution 3.054 · 1 distinct chain · 48% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase	protein	267	48% helix, 21% strand	A0A2N3Y640

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	517	0.69	0.79	58	SAH
2	436	0.66	0.79	55	SAH
3	218	0.52	0.77	28	empty
4	72	0.36	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 460 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7V6H · Crystal structure of the spnl · 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 A0A2N3Y640
Elsewhere: RCSB PDB 7V6H · PDBe 7V6H · UniProt A0A2N3Y640

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