MolNFT v1 · #167444 · protein

Crystal structure of the N-prenyltransferase daba in complex with ngg and MG2+

6VL1: “Crystal structure of the N-prenyltransferase daba in complex with ngg and MG2+”. X-ray diffraction, 2 ligands (R1V, MG), 4 pockets (best druggability 0.77). MolNFT v1 #167444 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6VL1
Type: protein
Length: 429 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Daba
UniProt: A0A386KZ50
Ligands: R1V, MG
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 68% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Daba	protein	429	68% helix, 6% strand	A0A386KZ50

Ligands and binding sites

R1V · N-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-L-glutamic acid · ligand · 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	203	0.77	0.92	43	MG, R1V
2	58	0.37	0.80	22	empty
3	60	0.28	0.73	16	empty
4	53	0.27	0.74	17	empty

Compared structures

6VL1 · Crystal Structure of the N-prenyltransferase DabA in Complex with NGG and Mg2+ · 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 6VL1 · PDBe 6VL1 · UniProt A0A386KZ50

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