MolNFT v1 · #10652 · protein + DNA
Ternary complex of T4 phage bgt with udp and a 13 mer DNA duplex
1IXY · 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)- 3': “Ternary complex of T4 phage bgt with udp and a 13 mer DNA duplex”. X-ray diffraction, 2 ligands (UDP, MG), 13 pockets (best druggability 0.85). MolNFT v1 #10652 on GenesisL1: 3D…
- PDB
- 1IXY
- Type
- protein + DNA
- Length
- 754 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)- 3'…
- EC
- 2.4.1.27
- UniProt
- P04547
- Ligands
- UDP, MG
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)- 3' | dna | 13 | — | — |
| E, F | 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3' | dna | 13 | — | — |
| A, B | DNA beta-glucosyltransferase (EC 2.4.1.27) | protein | 351 | 42% helix, 17% strand | P04547 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.85 | 0.94 | 47 | MG, UDP |
| 2 | 402 | 0.84 | 0.92 | 52 | MG, UDP |
| 3 | 775 | 0.79 | 0.83 | 51 | empty |
| 4 | 635 | 0.75 | 0.82 | 42 | empty |
| 5 | 324 | 0.70 | 0.84 | 37 | empty |
Interfaces
11 interfaces between chains.
- D–B · 617 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–A · 590 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–B · 583 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–E · 555 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- D–F · 519 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1IXY · Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex · 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 1IXY · PDBe 1IXY · UniProt P04547
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