Research workbench
Alpha-glucosyltransferase in complex with udp and a 13-mer DNA containing a central A:G mismatch
Analyse Alpha-glucosyltransferase in complex with udp and a 13-mer DNA containing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YA6
- Type
- protein + DNA
- Length
- 781 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*TP*AP*CP*TP*AP*AP*GP*AP*TP*AP*G)-3'; 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*T)-3'…
- EC
- 2.4.1.26
- UniProt
- P04519
- Ligands
- NCO, UDP
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*AP*TP*AP*CP*TP*AP*AP*GP*AP*TP*AP*G)-3' | dna | 12 | — | — |
| 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 | 380 | 39% helix, 20% strand | P04519 |
| B | DNA alpha-glucosyltransferase (EC 2.4.1.26) | protein | 377 | 38% helix, 19% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.84 | 0.86 | 90 | NCO, UDP |
| 2 | 669 | 0.84 | 0.88 | 64 | NCO, UDP |
| 3 | 223 | 0.56 | 0.79 | 32 | empty |
| 4 | 162 | 0.49 | 0.78 | 19 | empty |
| 5 | 148 | 0.48 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- D–A · 552 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 520 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- C–A · 486 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 397 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–B · 305 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 1YA6 · alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a central A:G… · 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 1YA6 · PDBe 1YA6 · UniProt P04519
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