MolNFT v1 · #51773 · protein
P4 protein from bacteriophage PHI12 N234G mutant in complex with ampcpp and mn
2VHC · NTPase P4: “P4 protein from bacteriophage PHI12 N234G mutant in complex with ampcpp and mn”. X-ray diffraction, 2 ligands (APC, MN), 11 pockets (best druggability 0.79). MolNFT v1 #51773 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VHC
- 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
- APC, MN
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | NTPase P4 | protein | 288 | 30% helix, 31% strand | Q94M05 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.79 | 0.81 | 97 | empty |
| 2 | 690 | 0.77 | 0.82 | 62 | empty |
| 3 | 328 | 0.75 | 0.87 | 37 | APC, MN |
| 4 | 251 | 0.75 | 0.89 | 33 | APC, MN |
| 5 | 267 | 0.59 | 0.79 | 39 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1929 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1808 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2VHC · P4 PROTEIN FROM BACTERIOPHAGE PHI12 N234G mutant in complex with AMPCPP and MN · 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 2VHC · PDBe 2VHC · UniProt Q94M05
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