MolNFT v1 · #152277 · protein
Pseudomonas putida CBB5 ndma with theophylline
6ICO · Methylxanthine N1-demethylase ndma: “Pseudomonas putida CBB5 ndma with theophylline”. X-ray diffraction, 3 ligands (FES, TEP, CO), 10 pockets (best druggability 0.81). MolNFT v1 #152277 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ICO
- 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, TEP, CO
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 30% 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, 30% strand | H9N289 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
- TEP · Theophylline · 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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.81 | 0.99 | 22 | TEP |
| 2 | 99 | 0.80 | 0.99 | 22 | TEP |
| 3 | 97 | 0.77 | 0.97 | 22 | TEP |
| 4 | 61 | 0.51 | 0.86 | 23 | empty |
| 5 | 167 | 0.50 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1141 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1138 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1123 Ų buried · 18 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 6ICO · PDBe 6ICO · UniProt H9N289
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