MolNFT v1 · #152273 · protein

Pseudomonas putida CBB5 ndma

6ICK · Methylxanthine N1-demethylase ndma: “Pseudomonas putida CBB5 ndma”. X-ray diffraction, 2 ligands (FES, FE), 12 pockets (best druggability 0.76). MolNFT v1 #152273 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ICK
Type: protein
Length: 990 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylxanthine N1-demethylase ndma
EC: 1.14.13.178
UniProt: H9N289
Ligands: FES, FE
Pockets: 12 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Methylxanthine N1-demethylase ndma (EC 1.14.13.178)	protein	330	25% helix, 31% strand	H9N289

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
FE · Fe (III) ion · metal · 3 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	445	0.76	0.84	42	empty
2	439	0.73	0.83	39	empty
3	437	0.72	0.82	48	empty
4	105	0.71	0.93	30	empty
5	62	0.71	0.97	25	empty

Interfaces

3 interfaces between chains.

A–C · 1084 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1064 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1054 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6ICK · Pseudomonas putida CBB5 NdmA · the same entry in another collection · chain A against A, TM-score 1.00
H9N289 · AlphaFold monomer V2.0 prediction for methylxanthine N1-demethylase ndma (H9N289) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 H9N289
Elsewhere: RCSB PDB 6ICK · PDBe 6ICK · UniProt H9N289

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