MolNFT v1 · #153356 · protein + DNA
Crystal structure of streptococcus pneumoniae fabt in complex with DNA
6JBX · Fatty acid biosynthesis transcriptional regulator: “Crystal structure of streptococcus pneumoniae fabt in complex with DNA”. X-ray diffraction, 1 ligand (TRD), 5 pockets (best druggability 0.87). MolNFT v1 #153356 on GenesisL1: 3D…
- PDB
- 6JBX
- Type
- protein + DNA
- Length
- 335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid biosynthesis transcriptional regulator; DNA (5'…
- UniProt
- A0A062WM61
- Ligands
- TRD
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fatty acid biosynthesis transcriptional regulator | protein | 146 | 68% helix, 7% strand | A0A062WM61 |
| B | Fatty acid biosynthesis transcriptional regulator | protein | 143 | 69% helix, 8% strand | A0A062WM61 |
| C | DNA (5'- D(*AP*AP*TP*AP*GP*TP*TP*TP*GP*AP*CP*TP*GP*TP*CP*AP*AP*AP*TP*TP*AP*TP* G)-3') | dna | 23 | — | — |
| D | DNA (5'- D(*CP*AP*TP*AP*AP*TP*TP*TP*GP*AP*CP*AP*GP*TP*CP*AP*AP*AP*CP*TP*AP*TP* T)-3') | dna | 23 | — | — |
Ligands and binding sites
- TRD · Tridecane · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.87 | 0.91 | 75 | TRD |
| 2 | 438 | 0.75 | 0.84 | 41 | empty |
| 3 | 53 | 0.32 | 0.77 | 11 | empty |
| 4 | 58 | 0.30 | 0.76 | 16 | empty |
| 5 | 61 | 0.25 | 0.72 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2681 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 996 Ų buried · 98 hydrogen bonds · nucleic-nucleic
- A–C · 535 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 502 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 468 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 6JBX · Crystal structure of Streptococcus pneumoniae FabT in complex with 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 A0A062WM61
- Elsewhere: RCSB PDB 6JBX · PDBe 6JBX · UniProt A0A062WM61
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