MolNFT v1 · #173627 · protein + DNA
S. agalactiae busr in complex with its busab-promotor DNA
7B5Y · Gntr family transcriptional regulator: “S. agalactiae busr in complex with its busab-promotor DNA”. Electron microscopy, 1 ligand (2BA), 16 pockets (best druggability 0.79). MolNFT v1 #173627 on GenesisL1: 3D structure, binding…
- PDB
- 7B5Y
- Type
- protein + DNA
- Length
- 910 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gntr family transcriptional regulator; Busr binding site in the busab promotor. STRAND1…
- UniProt
- K0JNC6
- Ligands
- 2BA
- Pockets
- 16 · best druggability 0.79
Structure
electron microscopy · 6 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Gntr family transcriptional regulator | protein | 203 | 48% helix, 14% strand | K0JNC6 |
| A | Gntr family transcriptional regulator | protein | 206 | 52% helix, 17% strand | K0JNC6 |
| B | Gntr family transcriptional regulator | protein | 204 | 52% helix, 14% strand | K0JNC6 |
| D | Gntr family transcriptional regulator | protein | 205 | 49% helix, 15% strand | K0JNC6 |
| E | Busr binding site in the busab promotor. STRAND1 | dna | 46 | — | — |
| F | Busr binding site in the busab promotor. STRAND2 | dna | 46 | — | — |
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 C, A, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.79 | 0.82 | 71 | empty |
| 2 | 944 | 0.76 | 0.79 | 52 | empty |
| 3 | 332 | 0.74 | 0.86 | 24 | 2BA |
| 4 | 335 | 0.73 | 0.85 | 24 | 2BA |
| 5 | 383 | 0.62 | 0.78 | 35 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2083 Ų buried · 221 hydrogen bonds · nucleic-nucleic
- C–A · 1599 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1586 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1455 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 1327 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7B5Y · S. agalactiae BusR in complex with its busAB-promotor DNA · the same entry in another collection · chain C against C, 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 7B5Y · PDBe 7B5Y · UniProt K0JNC6
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