MolNFT v1 · #152276 · protein
Pseudomonas putida CBB5 ndma with caffeine
6ICN · Methylxanthine N1-demethylase ndma: “Pseudomonas putida CBB5 ndma with caffeine”. X-ray diffraction, 3 ligands (FES, CFF, CO), 9 pockets (best druggability 0.80). MolNFT v1 #152276 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ICN
- Type
- protein
- Length
- 1,032 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, CO
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Methylxanthine N1-demethylase ndma (EC 1.14.13.178) | protein | 344 | 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
- CO · Cobalt (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.80 | 0.99 | 20 | CFF |
| 2 | 90 | 0.79 | 0.99 | 21 | CFF |
| 3 | 87 | 0.78 | 0.99 | 20 | CFF |
| 4 | 216 | 0.55 | 0.78 | 24 | empty |
| 5 | 160 | 0.49 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1177 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1141 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1137 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
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 6ICN · PDBe 6ICN · UniProt H9N289
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