MolNFT v1 · #189626 · protein + DNA
Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (trimer of dimers)
7VO0 · DNA_NT (84-mer): “Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (trimer of dimers)”. Electron microscopy, 1 ligand (ZN), 18 pockets (best druggability 0.75). MolNFT v1 #189626 on GenesisL1: 3D structure…
- PDB
- 7VO0
- Type
- protein + DNA
- Length
- 872 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA_NT (84-mer); DNA_T (84-mer); Putative metal uptake regulation protein
- UniProt
- Q9L2H5
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.75
Structure
electron microscopy · 3 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA_NT (84-mer) | dna | 43 | — | — |
| B | DNA_T (84-mer) | dna | 43 | — | — |
| G, H, K, L, M, N | Putative metal uptake regulation protein | protein | 131 | 42% helix, 21% strand | Q9L2H5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 18 copies · chains G, H, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.75 | 0.80 | 85 | empty |
| 2 | 1092 | 0.72 | 0.76 | 80 | empty |
| 3 | 1111 | 0.72 | 0.76 | 79 | empty |
| 4 | 876 | 0.72 | 0.77 | 66 | empty |
| 5 | 69 | 0.64 | 0.92 | 19 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1986 Ų buried · 151 hydrogen bonds · nucleic-nucleic
- K–L · 1435 Ų buried · 25 hydrogen bonds · protein-protein
- M–N · 1420 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1408 Ų buried · 14 hydrogen bonds · protein-protein
- B–N · 474 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 7VO0 · Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (trimer of… · 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 Q9L2H5
- Elsewhere: RCSB PDB 7VO0 · PDBe 7VO0 · UniProt Q9L2H5
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