Research workbench
P4 protein from bacteriophage PHI12 in complex with UTP
Analyse P4 protein from bacteriophage PHI12 in complex with UTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BLR
- Type
- protein
- Length
- 894 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NTPase P4
- UniProt
- Q94M05
- Ligands
- UTP
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NTPase P4 | protein | 297 | 31% helix, 31% strand | Q94M05 |
| C | NTPase P4 | protein | 300 | 33% helix, 30% strand | Q94M05 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 3 copies · chains A, B, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.81 | 0.84 | 90 | empty |
| 2 | 616 | 0.78 | 0.84 | 62 | UTP |
| 3 | 783 | 0.78 | 0.81 | 74 | empty |
| 4 | 392 | 0.77 | 0.87 | 45 | UTP |
| 5 | 364 | 0.56 | 0.75 | 50 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1880 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1854 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4BLR · P4 protein from bacteriophage PHI12 in complex with UTP · 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 4BLR · PDBe 4BLR · UniProt Q94M05
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