Research workbench
Crystal structure of klebsiella pneumoniae pmra in complex with pmra box DNA
Analyse Crystal structure of klebsiella pneumoniae pmra in complex with pmra box DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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