MolNFT v1 · #65011 · protein

Crystal structure of dicamba monooxygenase

3GKE · Ddmc: “Crystal structure of dicamba monooxygenase”. X-ray diffraction, 3 ligands (FES, FE, OXY), 12 pockets (best druggability 0.84). MolNFT v1 #65011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3GKE
Type: protein
Length: 988 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ddmc
UniProt: Q5S3I3
Ligands: FES, FE, OXY
Pockets: 12 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ddmc	protein	340	31% helix, 32% strand	Q5S3I3
B	Ddmc	protein	334	30% helix, 32% strand	Q5S3I3
C	Ddmc	protein	314	26% helix, 34% strand	Q5S3I3

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
FE · Fe (III) ion · metal · 2 copies · chains A, B
OXY · Oxygen molecule · ion · chains B
EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C
ACT · Acetate ion · additive · 4 copies · chains A, B, C

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

Pockets

12 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	278	0.84	0.95	50	OXY, ACT, EDO
2	168	0.82	0.97	44	ACT
3	293	0.61	0.79	34	empty
4	328	0.58	0.77	47	empty
5	243	0.57	0.79	25	empty

Interfaces

3 interfaces between chains.

A–C · 1172 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1152 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 982 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3GKE · Crystal Structure of Dicamba Monooxygenase · the same entry in another collection · chain A against A, TM-score 1.00
Q5S3I3 · AlphaFold monomer V2.0 prediction for dicamba O-demethylase, oxygenase component (Q5S3I3) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q5S3I3
Elsewhere: RCSB PDB 3GKE · PDBe 3GKE · UniProt Q5S3I3

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