Research workbench
Structure of lactococcus lactis zitr, C30S mutant in complex with DNA
Analyse Structure of lactococcus lactis zitr, C30S mutant in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YI3
- Type
- protein + DNA
- Length
- 1,286 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 0.77
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc transport transcriptional regulator | protein | 146 | 60% helix, 4% strand | Q9CDU5 |
| B, M, N | Zinc transport transcriptional regulator | protein | 144 | 63% helix, 6% strand | Q9CDU5 |
| C, G, K, O, P, L, H, D | DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)- 3') | dna | 16 | — | — |
| E, F, I, J | Zinc transport transcriptional regulator | protein | 145 | 63% helix, 5% strand | Q9CDU5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 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 | 813 | 0.77 | 0.81 | 69 | empty |
| 2 | 699 | 0.75 | 0.81 | 65 | empty |
| 3 | 805 | 0.75 | 0.80 | 71 | empty |
| 4 | 565 | 0.73 | 0.81 | 60 | empty |
| 5 | 552 | 0.66 | 0.77 | 49 | empty |
Interfaces
43 interfaces between chains.
- I–J · 2388 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 2304 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 2290 Ų buried · 4 hydrogen bonds · protein-protein
- M–N · 2182 Ų buried · 5 hydrogen bonds · protein-protein
- O–P · 682 Ų buried · 65 hydrogen bonds · nucleic-nucleic
Compared structures
- 5YI3 · Structure of Lactococcus lactis ZitR, C30S mutant 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 5YI3 · PDBe 5YI3 · UniProt Q9CDU5
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