Research workbench
Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (trimer of dimers)
Analyse Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.