Research workbench

Pseudomonas putida CBB5 ndma ql mutant with caffeine

Analyse Pseudomonas putida CBB5 ndma ql mutant with caffeine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ICP
Type: protein
Length: 1,003 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, CFF, FE
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methylxanthine N1-demethylase ndma (EC 1.14.13.178)	protein	335	24% helix, 30% strand	H9N289
B, C	Methylxanthine N1-demethylase ndma (EC 1.14.13.178)	protein	334	24% helix, 31% strand	H9N289

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
CFF · Caffeine · 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

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	568	0.77	0.84	68	FE, CFF
2	512	0.76	0.84	73	CFF
3	400	0.72	0.83	41	FE, CFF
4	61	0.69	0.96	25	empty
5	191	0.56	0.80	30	empty

Interfaces

3 interfaces between chains.

B–C · 1134 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1103 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1091 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

6ICP · Pseudomonas putida CBB5 NdmA QL mutant with caffeine · 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 6ICP · PDBe 6ICP · UniProt H9N289

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