MolNFT v1 · #178948 · protein
The phi-28 GP11 DNA packaging motor
7JQP · Encapsidation protein: “The phi-28 GP11 DNA packaging motor”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.88). MolNFT v1 #178948 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JQP
- Type
- protein
- Length
- 1,808 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Encapsidation protein
- UniProt
- B1ABI1
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Encapsidation protein | protein | 364 | 33% helix, 26% strand | B1ABI1 |
| B | Encapsidation protein | protein | 360 | 33% helix, 27% strand | B1ABI1 |
| C | Encapsidation protein | protein | 362 | 33% helix, 27% strand | B1ABI1 |
| D, E | Encapsidation protein | protein | 361 | 32% helix, 26% strand | B1ABI1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.88 | 0.90 | 151 | SO4 |
| 2 | 1050 | 0.84 | 0.85 | 97 | SO4 |
| 3 | 1107 | 0.84 | 0.85 | 129 | SO4 |
| 4 | 721 | 0.80 | 0.84 | 68 | empty |
| 5 | 875 | 0.79 | 0.82 | 97 | SO4 |
Interfaces
5 interfaces between chains.
- A–E · 2174 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2142 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2097 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 2063 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1695 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 7JQP · 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 7JQP · PDBe 7JQP · UniProt B1ABI1
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