Research workbench
A fusion protein of a beta helix region of gene product 5 and the foldon region of bacteriophage T4
Analyse A fusion protein of a beta helix region of gene product 5 and the foldon region… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A1M
- Type
- protein
- Length
- 590 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of thrombin cleavage site, tail-associated lysozyme, fibritin
- EC
- 3.2.1.17
- UniProt
- P16009, P10104
- Ligands
- K
- Pockets
- 2 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chimera of thrombin cleavage site, tail-associated lysozyme, fibritin (EC 3.2.1.17) | protein | 112 | 0% helix, 61% strand | P16009, P10104 |
| C | Chimera of thrombin cleavage site, tail-associated lysozyme, fibritin (EC 3.2.1.17) | protein | 111 | 0% helix, 61% strand | P16009, P10104 |
| D, E, F | Chimera of thrombin cleavage site, tail-associated lysozyme, fibritin (EC 3.2.1.17) | protein | 85 | 0% helix, 66% strand | P16009, P10104 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.89 | 0.90 | 112 | empty |
| 2 | 153 | 0.51 | 0.79 | 28 | empty |
Interfaces
12 interfaces between chains.
- B–C · 3871 Ų buried · 97 hydrogen bonds · protein-protein
- A–B · 3832 Ų buried · 99 hydrogen bonds · protein-protein
- A–C · 3730 Ų buried · 97 hydrogen bonds · protein-protein
- D–F · 3296 Ų buried · 89 hydrogen bonds · protein-protein
- D–E · 3285 Ų buried · 89 hydrogen bonds · protein-protein
Compared structures
- 3A1M · A fusion protein of a beta helix region of gene product 5 and the foldon region of… · 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 P16009
- Every structure of UniProt P10104
- Elsewhere: RCSB PDB 3A1M · PDBe 3A1M · UniProt P16009 · UniProt P10104
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.