Research workbench
The bacteriophage phi-29 viral genome packaging motor assembly
Analyse The bacteriophage phi-29 viral genome packaging motor assembly in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JQQ
- Type
- protein + DNA + RNA
- Length
- 2,340 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA packaging protein; Prna (117-mer); DNA (60-mer)
- EC
- 3.6.4.-
- UniProt
- P11014
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 30% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | DNA packaging protein (EC 3.6.4.-) | protein | 327 | 30% helix, 16% strand | P11014 |
| K, L, M, N, O | Prna (117-mer) | rna | 117 | — | — |
| F | DNA (60-mer) | dna | 60 | — | — |
| G | DNA (60-mer) | dna | 60 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.87 | 0.88 | 119 | empty |
| 2 | 504 | 0.85 | 0.90 | 63 | empty |
| 3 | 741 | 0.80 | 0.84 | 86 | AGS, MG |
| 4 | 138 | 0.79 | 0.96 | 25 | empty |
| 5 | 1030 | 0.79 | 0.80 | 88 | empty |
Interfaces
26 interfaces between chains.
- F–G · 2902 Ų buried · 255 hydrogen bonds · nucleic-nucleic
- B–C · 1828 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1652 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1533 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 1434 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7JQQ · The bacteriophage Phi-29 viral genome packaging motor assembly · 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 P11014
- Elsewhere: RCSB PDB 7JQQ · PDBe 7JQQ · UniProt P11014
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