Research workbench
Pseudomonas putida CBB5 ndma ql mutant with theobromine
Analyse Pseudomonas putida CBB5 ndma ql mutant with theobromine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ICQ
- Type
- protein
- Length
- 1,001 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, 37T, FE
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylxanthine N1-demethylase ndma (EC 1.14.13.178) | protein | 334 | 25% helix, 31% strand | H9N289 |
| B | Methylxanthine N1-demethylase ndma (EC 1.14.13.178) | protein | 333 | 25% helix, 30% strand | H9N289 |
| C | Methylxanthine N1-demethylase ndma (EC 1.14.13.178) | protein | 334 | 25% helix, 31% strand | H9N289 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
- 37T · Theobromine · 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
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.71 | 0.96 | 25 | empty |
| 2 | 351 | 0.71 | 0.83 | 40 | 37T |
| 3 | 91 | 0.70 | 0.94 | 28 | empty |
| 4 | 379 | 0.70 | 0.82 | 41 | 37T |
| 5 | 123 | 0.68 | 0.90 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1098 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1095 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1063 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6ICQ · Pseudomonas putida CBB5 NdmA QL mutant with theobromine · 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 C 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 6ICQ · PDBe 6ICQ · UniProt H9N289
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