MolNFT v1 · #152275 · protein
Pseudomonas putida CBB5 ndma with ferredoxin domain of ndmd
6ICM · Methylxanthine N1-demethylase ndma: “Pseudomonas putida CBB5 ndma with ferredoxin domain of ndmd”. X-ray diffraction, 2 ligands (FES, FE), 12 pockets (best druggability 0.73). MolNFT v1 #152275 on GenesisL1: 3D structure, binding…
- PDB
- 6ICM
- Type
- protein
- Length
- 1,077 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylxanthine N1-demethylase ndma; Oxidoreductase ndmd
- EC
- 1.14.13.178
- UniProt
- H9N289, H9N291
- Ligands
- FES, FE
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Methylxanthine N1-demethylase ndma (EC 1.14.13.178) | protein | 330 | 24% helix, 30% strand | H9N289 |
| D | Oxidoreductase ndmd | protein | 87 | 13% helix, 25% strand | H9N291 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · chains B, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.73 | 0.82 | 48 | FE |
| 2 | 420 | 0.72 | 0.82 | 44 | FE |
| 3 | 426 | 0.71 | 0.82 | 49 | FE |
| 4 | 286 | 0.59 | 0.78 | 31 | empty |
| 5 | 76 | 0.53 | 0.86 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1144 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1118 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1092 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 507 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 189 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6ICM · Pseudomonas putida CBB5 NdmA with ferredoxin domain of NdmD · 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 0.99
- H9N291 · AlphaFold monomer V2.0 prediction for oxidoreductase ndmd (H9N291) · a predicted model of the same protein · chain D against A, TM-score 0.97
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
- Every structure of UniProt H9N291
- Elsewhere: RCSB PDB 6ICM · PDBe 6ICM · UniProt H9N289 · UniProt H9N291
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