MolNFT v1 · #28183 · protein + DNA
Alpha-glucosyltransferase in complex with udp-glucose and DNA containing an abasic site
1Y6F · 5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3': “Alpha-glucosyltransferase in complex with udp-glucose and DNA containing an abasic site”. X-ray diffraction, 2 ligands (UPG, UDP), 8 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 1Y6F
- Type
- protein + DNA
- Length
- 814 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3'…
- EC
- 2.4.1.26
- UniProt
- P04519
- Ligands
- UPG, UDP
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3' | dna | 13 | — | — |
| D | 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3' | dna | 13 | — | — |
| A | DNA alpha-glucosyltransferase (EC 2.4.1.26) | protein | 394 | 43% helix, 19% strand | P04519 |
| B | DNA alpha-glucosyltransferase (EC 2.4.1.26) | protein | 394 | 40% helix, 19% strand | P04519 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · chains A
- UDP · Uridine-5'-diphosphate · ligand · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.80 | 0.81 | 104 | UPG |
| 2 | 573 | 0.79 | 0.85 | 59 | UDP, GOL |
| 3 | 162 | 0.50 | 0.78 | 19 | empty |
| 4 | 136 | 0.46 | 0.77 | 19 | empty |
| 5 | 142 | 0.42 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–A · 735 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 544 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- D–A · 494 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 340 Ų buried · 3 hydrogen bonds · protein-nucleic
- D–B · 214 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1Y6F · alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site · 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 P04519
- Elsewhere: RCSB PDB 1Y6F · PDBe 1Y6F · UniProt P04519
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