MolNFT v1 · #153254 · protein
Crystal structure of hind with nmft and no
6J87 · Nocardicin N-oxygenase: “Crystal structure of hind with nmft and no”. X-ray diffraction, 3 ligands (HEM, B9L, NO), 11 pockets (best druggability 0.87). MolNFT v1 #153254 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6J87
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nocardicin N-oxygenase
- UniProt
- A0A1M4Y7D5
- Ligands
- HEM, B9L, NO
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nocardicin N-oxygenase | protein | 395 | 53% helix, 11% strand | A0A1M4Y7D5 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- B9L · N-[(2S)-1-hydroxy-3-(1H-indol-3-yl)propan-2-yl]-Nalpha-methyl-L-phenylalaninamide · ligand · 2 copies · chains A, B
- NO · Nitric oxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.87 | 0.92 | 62 | HEM, NO, B9L |
| 2 | 614 | 0.87 | 0.91 | 62 | HEM, NO, B9L |
| 3 | 792 | 0.77 | 0.81 | 78 | empty |
| 4 | 207 | 0.57 | 0.79 | 23 | empty |
| 5 | 203 | 0.54 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 902 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6J87 · Crystal structure of HinD with NMFT and NO · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1M4Y7D5
- Elsewhere: RCSB PDB 6J87 · PDBe 6J87 · UniProt A0A1M4Y7D5
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