MolNFT v1 · #112382 · protein
Crystal structure of the bacteriophage G20C portal protein
4ZJN: “Crystal structure of the bacteriophage G20C portal protein”. X-ray diffraction, 18 pockets (best druggability 0.88). MolNFT v1 #112382 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZJN
- Type
- protein
- Length
- 1,233 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Portal protein
- UniProt
- A7XXR3
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Portal protein | protein | 413 | 46% helix, 16% strand | A7XXR3 |
| B | Portal protein | protein | 411 | 46% helix, 18% strand | A7XXR3 |
| C | Portal protein | protein | 409 | 46% helix, 17% strand | A7XXR3 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.88 | 0.90 | 119 | empty |
| 2 | 684 | 0.85 | 0.89 | 80 | empty |
| 3 | 997 | 0.81 | 0.83 | 94 | MPD |
| 4 | 336 | 0.81 | 0.91 | 47 | empty |
| 5 | 385 | 0.70 | 0.82 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5647 Ų buried · 69 hydrogen bonds · protein-protein
- B–C · 5606 Ų buried · 67 hydrogen bonds · protein-protein
- A–C · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZJN · Crystal structure of the bacteriophage G20C portal protein · 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 A7XXR3
- Elsewhere: RCSB PDB 4ZJN · PDBe 4ZJN · UniProt A7XXR3
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