MolNFT v1 · #116433 · protein + DNA
The structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi in complex with target double strand DNA
5DDG: “The structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi in complex with target…”. X-ray diffraction, 12 pockets (best druggability 0.63). MolNFT v1 #116433 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DDG
- Type
- protein + DNA
- Length
- 503 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional factor arar; DNA (27-mer)
- UniProt
- Q8AAV8
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional factor arar | protein | 226 | 33% helix, 29% strand | Q8AAV8 |
| B | Transcriptional factor arar | protein | 223 | 33% helix, 30% strand | Q8AAV8 |
| C | DNA (27-mer) | dna | 27 | — | — |
| D | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- MLA · Malonic acid · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.63 | 0.80 | 30 | MLA |
| 2 | 110 | 0.57 | 0.85 | 29 | MLA |
| 3 | 276 | 0.53 | 0.75 | 25 | empty |
| 4 | 116 | 0.38 | 0.75 | 24 | empty |
| 5 | 106 | 0.37 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1572 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1191 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- B–D · 614 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 609 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 507 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 5DDG · The structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in… · 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 Q8AAV8
- Elsewhere: RCSB PDB 5DDG · PDBe 5DDG · UniProt Q8AAV8
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