MolNFT v1 · #51787 · protein
P4 protein from bacteriophage PHI12 K241C mutant in complex with ADP and mgcl
2VHU · NTPase P4: “P4 protein from bacteriophage PHI12 K241C mutant in complex with ADP and mgcl”. X-ray diffraction, 2 ligands (ADP, MG), 5 pockets (best druggability 0.80). MolNFT v1 #51787 on GenesisL1: 3D structure, binding sites and…
- 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
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