MolNFT v1 · #106474 · protein + DNA
Crystal structure of klebsiella pneumoniae pmra in complex with pmra box DNA
4S05 · DNA-binding transcriptional regulator basr: “Crystal structure of klebsiella pneumoniae pmra in complex with pmra box DNA”. X-ray diffraction, 2 ligands (BEF, MG), 8 pockets (best druggability 0.70). MolNFT v1 #106474 on GenesisL1…
- PDB
- 4S05
- Type
- protein + DNA
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding transcriptional regulator basr; DNA (26-mer)
- UniProt
- S5YJU7
- Ligands
- BEF, MG
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-binding transcriptional regulator basr | protein | 219 | 42% helix, 16% strand | S5YJU7 |
| C | DNA (26-mer) | dna | 26 | — | — |
| D | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.70 | 0.97 | 15 | empty |
| 2 | 370 | 0.62 | 0.78 | 41 | empty |
| 3 | 442 | 0.59 | 0.75 | 33 | empty |
| 4 | 143 | 0.54 | 0.81 | 23 | empty |
| 5 | 186 | 0.50 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1452 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1124 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–C · 520 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 470 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 454 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4S05 · Crystal structure of Klebsiella pneumoniae PmrA in complex with PmrA box 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 S5YJU7
- Elsewhere: RCSB PDB 4S05 · PDBe 4S05 · UniProt S5YJU7
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