Research workbench
P4 protein from bacteriophage PHI12 in complex with ampcpp and mg
Analyse P4 protein from bacteriophage PHI12 in complex with ampcpp and mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W49
- Type
- protein
- Length
- 912 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NTPase P4
- UniProt
- Q94M05
- Ligands
- APC, MG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | NTPase P4 | protein | 304 | 32% helix, 30% strand | Q94M05 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.78 | 0.83 | 66 | empty |
| 2 | 748 | 0.77 | 0.81 | 67 | empty |
| 3 | 664 | 0.76 | 0.82 | 76 | empty |
| 4 | 311 | 0.74 | 0.87 | 39 | APC, MG |
| 5 | 331 | 0.74 | 0.86 | 45 | APC, MG |
Interfaces
2 interfaces between chains.
- B–C · 1946 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1941 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1W49 · P4 protein from Bacteriophage PHI12 in complex with AMPcPP and Mg · 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 1W49 · PDBe 1W49 · UniProt Q94M05
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