MolNFT v1 · #152274 · protein

Pseudomonas putida CBB5 ndmb

6ICL · Methylxanthine N3-demethylase ndmb: “Pseudomonas putida CBB5 ndmb”. X-ray diffraction, 2 ligands (FES, FE), 3 pockets (best druggability 0.67). MolNFT v1 #152274 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ICL
Type: protein
Length: 338 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylxanthine N3-demethylase ndmb
EC: 1.14.13.179
UniProt: H9N290
Ligands: FES, FE
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methylxanthine N3-demethylase ndmb (EC 1.14.13.179)	protein	338	23% helix, 34% strand	H9N290

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · chains A
FE · Fe (III) ion · metal · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.67	0.81	39	empty
2	291	0.63	0.80	32	empty
3	55	0.35	0.78	16	empty

Compared structures

6ICL · Pseudomonas putida CBB5 NdmB · the same entry in another collection · chain A against A, TM-score 1.00
H9N290 · AlphaFold monomer V2.0 prediction for methylxanthine N3-demethylase ndmb (H9N290) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 H9N290
Elsewhere: RCSB PDB 6ICL · PDBe 6ICL · UniProt H9N290

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