MolNFT v1 · #83700 · protein

Crystal structure of RV3378C with inhibitor bph-629

3WQM · Diterpene synthase: “Crystal structure of RV3378C with inhibitor bph-629”. X-ray diffraction, 3 ligands (B29, MG, PO4), 2 pockets (best druggability 0.74). MolNFT v1 #83700 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3WQM
Type: protein
Length: 294 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diterpene synthase
EC: 3.1.7.9, 3.1.7.8
UniProt: O50407
Ligands: B29, MG, PO4
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diterpene synthase (EC 3.1.7.9, 3.1.7.8)	protein	294	51% helix, 14% strand	O50407

Ligands and binding sites

B29 · [2-(3-dibenzofuran-4-yl-phenyl)-1-hydroxy-1-phosphono-ethyl]-phosphonic acid · ligand · 2 copies · chains A
MG · Magnesium ion · metal · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A

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

Pockets

2 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	503	0.74	0.82	53	B29, MG
2	125	0.43	0.76	25	empty

Compared structures

3WQM · Crystal structure of Rv3378c with inhibitor BPH-629 · 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 O50407
Elsewhere: RCSB PDB 3WQM · PDBe 3WQM · UniProt O50407

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