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Crystal structure of the N-prenyltransferase daba in complex with gspp and MN2+

Analyse Crystal structure of the N-prenyltransferase daba in complex with gspp and MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VL0
Type: protein
Length: 429 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Daba
UniProt: A0A386KZ50
Ligands: GST, MN, MG
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 68% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Daba	protein	429	68% helix, 5% strand	A0A386KZ50

Ligands and binding sites

GST · Geranyl S-thiolodiphosphate · ligand · chains A
MN · Manganese (II) ion · metal · chains A
MG · Magnesium ion · metal · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	209	0.79	0.93	42	GST, MG
2	52	0.38	0.81	19	empty
3	60	0.31	0.75	18	empty
4	58	0.30	0.75	18	empty

Compared structures

6VL0 · Crystal Structure of the N-prenyltransferase DabA in Complex with GSPP and Mn2+ · 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 A0A386KZ50
Elsewhere: RCSB PDB 6VL0 · PDBe 6VL0 · UniProt A0A386KZ50

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