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Crystal structure of a C-terminal domain of the bacteriophage P2 tail spike protein, gpv
Analyse Crystal structure of a C-terminal domain of the bacteriophage P2 tail spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AQJ
- Type
- protein
- Length
- 695 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate assembly protein V
- UniProt
- P31340
- Ligands
- FE2, CA, CL
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, R | Baseplate assembly protein V | protein | 117 | 0% helix, 61% strand | P31340 |
| B, P | Baseplate assembly protein V | protein | 114 | 0% helix, 61% strand | P31340 |
| Q | Baseplate assembly protein V | protein | 116 | 0% helix, 60% strand | P31340 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B, C, P, Q, R
- CA · Calcium ion · metal · 2 copies · chains A, B, C, P, Q, R
- CL · Chloride ion · ion · 2 copies · chains A, B, C, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.88 | 0.91 | 51 | empty |
| 2 | 650 | 0.88 | 0.92 | 51 | empty |
| 3 | 186 | 0.55 | 0.80 | 40 | empty |
| 4 | 182 | 0.47 | 0.76 | 27 | empty |
| 5 | 74 | 0.28 | 0.72 | 16 | empty |
Interfaces
15 interfaces between chains.
- P–R · 3808 Ų buried · 107 hydrogen bonds · protein-protein
- A–C · 3797 Ų buried · 107 hydrogen bonds · protein-protein
- A–B · 3762 Ų buried · 100 hydrogen bonds · protein-protein
- P–Q · 3674 Ų buried · 102 hydrogen bonds · protein-protein
- Q–R · 3668 Ų buried · 108 hydrogen bonds · protein-protein
Compared structures
- 3AQJ · Crystal Structure of a C-terminal domain of the bacteriophage P2 tail spike protein, gpV · 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 P31340
- Elsewhere: RCSB PDB 3AQJ · PDBe 3AQJ · UniProt P31340
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