Research workbench
P4 protein from bacteriophage PHI12 K241C mutant in complex with ADP and mgcl
Analyse P4 protein from bacteriophage PHI12 K241C mutant in complex with ADP and mgcl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VHU
- Type
- protein
- Length
- 864 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NTPase P4
- UniProt
- Q94M05
- Ligands
- ADP, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | NTPase P4 | protein | 288 | 27% helix, 31% strand | Q94M05 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.80 | 0.82 | 96 | empty |
| 2 | 767 | 0.78 | 0.82 | 78 | empty |
| 3 | 306 | 0.71 | 0.85 | 37 | ADP, MG |
| 4 | 440 | 0.71 | 0.82 | 52 | ADP, MG |
| 5 | 381 | 0.57 | 0.75 | 49 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1843 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1822 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2VHU · P4 PROTEIN FROM BACTERIOPHAGE PHI12 K241C mutant in complex with ADP and MgCl · 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 Q94M05
- Elsewhere: RCSB PDB 2VHU · PDBe 2VHU · UniProt Q94M05
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.