Research workbench
Alpha-glucosyltransferase in complex with udp and a 13_MER DNA containing a hmu base at 2.8 a resolution
Analyse Alpha-glucosyltransferase in complex with udp and a 13_MER DNA containing a hmu… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y6G
- Type
- protein + DNA
- Length
- 810 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*AP*TP*AP*CP*TP*(5HU)P*AP*GP*AP*TP*AP*G)-3'…
- EC
- 2.4.1.26
- UniProt
- P04519
- Ligands
- NCO, UDP, CL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*GP*AP*TP*AP*CP*TP*(5HU)P*AP*GP*AP*TP*AP*G)-3' | dna | 13 | — | — |
| D | 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*T)-3' | dna | 12 | — | — |
| A | DNA alpha-glucosyltransferase (EC 2.4.1.26) | protein | 392 | 39% helix, 19% strand | P04519 |
| B | DNA alpha-glucosyltransferase (EC 2.4.1.26) | protein | 393 | 42% helix, 18% strand | P04519 |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 7 copies · chains D, A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.85 | 0.86 | 110 | NCO, UDP |
| 2 | 641 | 0.83 | 0.87 | 75 | CL, NCO, UDP |
| 3 | 161 | 0.50 | 0.78 | 22 | empty |
| 4 | 163 | 0.50 | 0.78 | 23 | empty |
| 5 | 132 | 0.45 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 499 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- D–A · 475 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–A · 443 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 430 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–B · 285 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1Y6G · alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at… · 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 1Y6G · PDBe 1Y6G · UniProt P04519
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