MolNFT v1 · #112874 · protein
Streptomyces peucetius nitrososynthase dnmz in tdp-bound state
4ZYJ: “Streptomyces peucetius nitrososynthase dnmz in tdp-bound state”. X-ray diffraction, 1 ligand (TYD), 18 pockets (best druggability 0.86). MolNFT v1 #112874 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZYJ
- Type
- protein
- Length
- 1,551 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dnmz
- EC
- 1.14.13.187
- Ligands
- TYD
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dnmz (EC 1.14.13.187) | protein | 388 | 59% helix, 14% strand | — |
| B | Dnmz (EC 1.14.13.187) | protein | 380 | 57% helix, 12% strand | — |
| C | Dnmz (EC 1.14.13.187) | protein | 391 | 57% helix, 13% strand | — |
| D | Dnmz (EC 1.14.13.187) | protein | 392 | 58% helix, 14% strand | — |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.86 | 0.88 | 106 | empty |
| 2 | 1054 | 0.79 | 0.80 | 95 | TYD |
| 3 | 956 | 0.79 | 0.81 | 82 | TYD |
| 4 | 1111 | 0.78 | 0.80 | 93 | TYD |
| 5 | 845 | 0.77 | 0.81 | 75 | TYD |
Interfaces
6 interfaces between chains.
- B–D · 1858 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1843 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1442 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1424 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 149 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4ZYJ · Streptomyces peucetius nitrososynthase dnmZ in TDP-bound 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 4ZYJ · PDBe 4ZYJ
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