MolNFT v1 · #178933 · protein
The phi-28 GP11 DNA packaging motor
7JQ7 · Encapsidation protein: “The phi-28 GP11 DNA packaging motor”. X-ray diffraction, 2 ligands (IOD, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #178933 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JQ7
- Type
- protein
- Length
- 1,825 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Encapsidation protein
- UniProt
- B1ABI1
- Ligands
- IOD, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Encapsidation protein | protein | 366 | 32% helix, 26% strand | B1ABI1 |
| B, D, E | Encapsidation protein | protein | 364 | 31% helix, 26% strand | B1ABI1 |
| C | Encapsidation protein | protein | 367 | 31% helix, 26% strand | B1ABI1 |
Ligands and binding sites
- IOD · Iodide ion · ion · 131 copies · chains A, B, E, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains C, E
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 | 867 | 0.86 | 0.89 | 109 | IOD |
| 2 | 1013 | 0.86 | 0.87 | 103 | IOD |
| 3 | 1021 | 0.82 | 0.83 | 80 | IOD |
| 4 | 1171 | 0.81 | 0.82 | 99 | IOD |
| 5 | 569 | 0.76 | 0.83 | 59 | IOD |
Interfaces
5 interfaces between chains.
- B–C · 2242 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 2210 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2121 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1880 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1817 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 7JQ7 · The Phi-28 gp11 DNA packaging Motor · 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 B1ABI1
- Elsewhere: RCSB PDB 7JQ7 · PDBe 7JQ7 · UniProt B1ABI1
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