Research workbench
Ternary complex of T4 phage bgt with udp and a 13 mer DNA duplex
Analyse Ternary complex of T4 phage bgt with udp and a 13 mer DNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M5R
- 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
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% 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 | 41% helix, 18% strand | P04547 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 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
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.86 | 0.94 | 56 | UDP, TRS |
| 2 | 664 | 0.84 | 0.88 | 61 | UDP, TRS |
| 3 | 759 | 0.77 | 0.82 | 48 | empty |
| 4 | 592 | 0.73 | 0.81 | 43 | empty |
| 5 | 289 | 0.66 | 0.82 | 33 | empty |
Interfaces
10 interfaces between chains.
- C–A · 635 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–B · 586 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–F · 556 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–E · 527 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- E–A · 338 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1M5R · 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 1M5R · PDBe 1M5R · UniProt P04547
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