Research workbench
Bgt in complex with a 13MER DNA containing a central C:G base pair and udp
Analyse Bgt in complex with a 13MER DNA containing a central C:G base pair and udp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SXQ
- Type
- protein + DNA
- Length
- 754 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*TP*TP*T)-3'…
- EC
- 2.4.1.27
- UniProt
- P04547
- Ligands
- UDP
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*TP*TP*T)-3' | dna | 13 | — | — |
| E, F | 5'-D(*AP*AP*AP*AP*AP*AP*CP*TP*TP*TP*TP*TP*T)-3' | dna | 13 | — | — |
| A, B | DNA beta-glucosyltransferase (EC 2.4.1.27) | protein | 351 | 40% helix, 18% strand | P04547 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.82 | 0.85 | 83 | UDP |
| 2 | 899 | 0.82 | 0.84 | 68 | UDP |
| 3 | 112 | 0.45 | 0.78 | 22 | empty |
| 4 | 96 | 0.45 | 0.80 | 22 | empty |
| 5 | 134 | 0.44 | 0.76 | 23 | empty |
Interfaces
12 interfaces between chains.
- C–E · 512 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- D–F · 505 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- F–B · 407 Ų buried · 3 hydrogen bonds · protein-nucleic
- D–B · 378 Ų buried · 5 hydrogen bonds · protein-nucleic
- E–A · 376 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 1SXQ · BGT in complex with a 13mer DNA containing a central C:G base pair and UDP · 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 P04547
- Elsewhere: RCSB PDB 1SXQ · PDBe 1SXQ · UniProt P04547
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