MolNFT v1 · #140662 · protein + DNA
Structure of lactococcus lactis zitr, wild type in complex with DNA
5YI2 · Zinc transport transcriptional regulator: “Structure of lactococcus lactis zitr, wild type in complex with DNA”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.78). MolNFT v1 #140662 on GenesisL1: 3D structure…
- PDB
- 5YI2
- Type
- protein + DNA
- Length
- 1,291 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc transport transcriptional regulator; DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*A…
- UniProt
- Q9CDU5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, M | Zinc transport transcriptional regulator | protein | 146 | 64% helix, 5% strand | Q9CDU5 |
| B, F, I, J, N | Zinc transport transcriptional regulator | protein | 145 | 63% helix, 8% strand | Q9CDU5 |
| C, G, K, O, D, P, L, H | DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)- 3') | dna | 16 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, E, F, I, J, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.78 | 0.84 | 55 | empty |
| 2 | 566 | 0.77 | 0.84 | 56 | empty |
| 3 | 986 | 0.77 | 0.79 | 89 | empty |
| 4 | 885 | 0.76 | 0.80 | 78 | empty |
| 5 | 890 | 0.72 | 0.77 | 66 | empty |
Interfaces
46 interfaces between chains.
- E–F · 2354 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2327 Ų buried · 10 hydrogen bonds · protein-protein
- M–N · 2317 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 2238 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 696 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Compared structures
- 5YI2 · Structure of Lactococcus lactis ZitR, wild type in complex with DNA · 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 Q9CDU5
- Elsewhere: RCSB PDB 5YI2 · PDBe 5YI2 · UniProt Q9CDU5
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