MolNFT v1 · #84599 · protein + DNA
Crystal structure of SCO3205, a marr family transcriptional regulator from streptomyces coelicolor, in complex with DNA
3ZPL · Putative marr-family transcriptional repressor: “Crystal structure of SCO3205, a marr family transcriptional regulator from streptomyces coelicolor, in…”. X-ray diffraction, 1 ligand (PO4), 13 pockets (best druggability 0.89).…
- PDB
- 3ZPL
- Type
- protein + DNA
- Length
- 720 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative marr-family transcriptional repressor…
- UniProt
- Q9KYU1
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative marr-family transcriptional repressor | protein | 159 | 69% helix, 8% strand | Q9KYU1 |
| C, D, G, H | 5'-D(*AP*AP*AP*GP*AP*TP*TP*GP*AP*GP*AP*TP*CP*TP *CP*AP*AP*TP*CP*TP*TP*DT)-3' | dna | 22 | — | — |
| E | Putative marr-family transcriptional repressor | protein | 160 | 68% helix, 8% strand | Q9KYU1 |
| F | Putative marr-family transcriptional repressor | protein | 154 | 71% helix, 8% strand | Q9KYU1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.89 | 0.90 | 97 | empty |
| 2 | 684 | 0.86 | 0.90 | 70 | empty |
| 3 | 130 | 0.69 | 0.90 | 19 | empty |
| 4 | 120 | 0.48 | 0.80 | 18 | empty |
| 5 | 94 | 0.37 | 0.76 | 14 | empty |
Interfaces
16 interfaces between chains.
- E–F · 2797 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2750 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 936 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- C–D · 933 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- B–D · 620 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3ZPL · Crystal structure of Sco3205, a MarR family transcriptional regulator from Streptomyces… · 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 Q9KYU1
- Elsewhere: RCSB PDB 3ZPL · PDBe 3ZPL · UniProt Q9KYU1
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