MolNFT v1 · #28266 · protein + DNA
Alpha-glucosyltransferase in complex with udp and a 13-mer DNA containing a hmu base at 1.9 a resolution
1Y8Z · 5'-D(*GP*AP*TP*AP*CP*TP*(5HU)P*AP*GP*AP*TP*AP*G)-3': “Alpha-glucosyltransferase in complex with udp and a 13-mer DNA containing a hmu base at 1.9 a resolution”. X-ray diffraction, 3 ligands (NCO, UDP, CL), 8 pockets (best…
- PDB
- 1Y8Z
- Type
- protein + DNA
- Length
- 786 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'; 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*G)-3'…
- EC
- 2.4.1.26
- UniProt
- P04519
- Ligands
- NCO, UDP, CL
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% 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*G)-3' | dna | 9 | — | — |
| A | DNA alpha-glucosyltransferase (EC 2.4.1.26) | protein | 391 | 44% helix, 19% strand | P04519 |
| B | DNA alpha-glucosyltransferase (EC 2.4.1.26) | protein | 373 | 41% helix, 20% strand | P04519 |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 5 copies · chains D, A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.84 | 0.85 | 102 | UDP |
| 2 | 526 | 0.82 | 0.88 | 61 | CL, UDP |
| 3 | 139 | 0.46 | 0.77 | 18 | empty |
| 4 | 133 | 0.46 | 0.77 | 19 | empty |
| 5 | 110 | 0.43 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–A · 814 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–A · 588 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–B · 444 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–D · 385 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- D–B · 299 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified (artifact, nucleotide modification).
Compared structures
- 1Y8Z · alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a HMU base at… · 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 P04519
- Elsewhere: RCSB PDB 1Y8Z · PDBe 1Y8Z · UniProt P04519
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