MolNFT v1 · #81412 · protein + DNA
Crystal structure of the T4 phage SF1B helicase dda
3UPU · ATP-dependent DNA helicase dda: “Crystal structure of the T4 phage SF1B helicase dda”. X-ray diffraction, 17 pockets (best druggability 0.82). MolNFT v1 #81412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UPU
- Type
- protein + DNA
- Length
- 1,341 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase dda; 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'
- EC
- 3.6.4.12
- UniProt
- P32270
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | ATP-dependent DNA helicase dda (EC 3.6.4.12) | protein | 439 | 33% helix, 28% strand | P32270 |
| D, E, F | 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3' | dna | 8 | — | — |
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.82 | 0.84 | 84 | empty |
| 2 | 868 | 0.80 | 0.83 | 83 | empty |
| 3 | 949 | 0.80 | 0.82 | 88 | empty |
| 4 | 924 | 0.75 | 0.78 | 71 | empty |
| 5 | 1122 | 0.74 | 0.77 | 82 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1029 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 1020 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–F · 1017 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 457 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3UPU · Crystal structure of the T4 Phage SF1B Helicase Dda · 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 P32270
- Elsewhere: RCSB PDB 3UPU · PDBe 3UPU · UniProt P32270
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