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Mechanism for regulation of DNA binding of bordetella bronchiseptica bpsr by 6-hydroxynicotinic acid
Analyse Mechanism for regulation of DNA binding of bordetella bronchiseptica bpsr by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PCP
- Type
- protein
- Length
- 834 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Marr family transcriptional regulator
- UniProt
- A0A0T7MD48
- Ligands
- OA7
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Marr family transcriptional regulator | protein | 140 | 66% helix, 11% strand | A0A0T7MD48 |
| B | Marr family transcriptional regulator | protein | 135 | 67% helix, 7% strand | A0A0T7MD48 |
| C, E | Marr family transcriptional regulator | protein | 140 | 66% helix, 7% strand | A0A0T7MD48 |
| D | Marr family transcriptional regulator | protein | 139 | 66% helix, 8% strand | A0A0T7MD48 |
Ligands and binding sites
- OA7 · 6-hydroxypyridine-3-carboxylic acid · ligand · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.63 | 0.85 | 26 | OA7 |
| 2 | 125 | 0.63 | 0.86 | 24 | OA7 |
| 3 | 142 | 0.62 | 0.85 | 28 | OA7 |
| 4 | 176 | 0.61 | 0.83 | 28 | OA7 |
| 5 | 132 | 0.61 | 0.85 | 27 | OA7 |
Interfaces
7 interfaces between chains.
- A–D · 2386 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2355 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 2350 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 380 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 132 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6PCP · Mechanism for regulation of DNA binding of Bordetella bronchiseptica BpsR by… · 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 A0A0T7MD48
- Elsewhere: RCSB PDB 6PCP · PDBe 6PCP · UniProt A0A0T7MD48
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