Research workbench
P4 protein from bacteriophage PHI12 N234G mutant in complex with ampcpp and mn
Analyse P4 protein from bacteriophage PHI12 N234G mutant in complex with ampcpp and mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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