Research workbench
S. agalactiae busr in complex with its busa-promotor DNA
Analyse S. agalactiae busr in complex with its busa-promotor DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OZ3
- Type
- protein + DNA
- Length
- 892 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gntr family transcriptional regulator; PBUSA_REV; PBUSA_FOR
- UniProt
- K0JNC6
- Ligands
- 2BA
- Pockets
- 16 · best druggability 0.75
Structure
electron microscopy · 6 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gntr family transcriptional regulator | protein | 202 | 54% helix, 16% strand | K0JNC6 |
| B | Gntr family transcriptional regulator | protein | 203 | 52% helix, 15% strand | K0JNC6 |
| C | Gntr family transcriptional regulator | protein | 201 | 51% helix, 13% strand | K0JNC6 |
| D | Gntr family transcriptional regulator | protein | 198 | 51% helix, 15% strand | K0JNC6 |
| F | PBUSA_REV | dna | 44 | — | — |
| G | PBUSA_FOR | dna | 44 | — | — |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.75 | 0.86 | 24 | 2BA |
| 2 | 636 | 0.75 | 0.81 | 48 | empty |
| 3 | 351 | 0.74 | 0.85 | 25 | 2BA |
| 4 | 663 | 0.72 | 0.79 | 53 | empty |
| 5 | 300 | 0.57 | 0.76 | 41 | empty |
Interfaces
15 interfaces between chains.
- F–G · 2024 Ų buried · 205 hydrogen bonds · nucleic-nucleic
- B–D · 1804 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1732 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1338 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1337 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7OZ3 · S. agalactiae BusR in complex with its busA-promotor DNA · the same entry in another collection · chain B against B, 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 K0JNC6
- Elsewhere: RCSB PDB 7OZ3 · PDBe 7OZ3 · UniProt K0JNC6
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