Research workbench
Streptomyces peucetius nitrososynthase dnmz in ligand-free state
Analyse Streptomyces peucetius nitrososynthase dnmz in ligand-free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZXV
- Type
- protein
- Length
- 1,571 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dnmz
- EC
- 1.14.13.187
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dnmz (EC 1.14.13.187) | protein | 394 | 55% helix, 13% strand | — |
| B | Dnmz (EC 1.14.13.187) | protein | 391 | 56% helix, 12% strand | — |
| C | Dnmz (EC 1.14.13.187) | protein | 391 | 57% helix, 13% strand | — |
| D | Dnmz (EC 1.14.13.187) | protein | 395 | 55% helix, 13% strand | — |
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.83 | 0.90 | 67 | empty |
| 2 | 425 | 0.82 | 0.90 | 68 | empty |
| 3 | 724 | 0.80 | 0.84 | 71 | empty |
| 4 | 1084 | 0.78 | 0.80 | 103 | empty |
| 5 | 911 | 0.78 | 0.80 | 80 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1723 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1716 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1443 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1424 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 152 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ZXV · Streptomyces peucetius nitrososynthase DnmZ in ligand-free state · 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
- Elsewhere: RCSB PDB 4ZXV · PDBe 4ZXV
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