MolNFT v1 · #159828 · protein
Chimera of bacteriophage obp GP146 central spike protein and a T4 GP5 beta-helix fragment
6P2A · Chimera of bacteriophage obp GP146 and a T4 GP5: “Chimera of bacteriophage obp GP146 central spike protein and a T4 GP5 beta-helix fragment”. X-ray diffraction, 5 ligands (STE, ELA, PLM), 6 pockets (best druggability 0.86). MolNFT…
- PDB
- 6P2A
- Type
- protein
- Length
- 871 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of bacteriophage obp GP146 and a T4 GP5
- EC
- 3.2.1.17
- UniProt
- P16009, G9IA38
- Ligands
- STE, ELA, PLM, FE2, MG
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Chimera of bacteriophage obp GP146 and a T4 GP5 (EC 3.2.1.17) | protein | 145 | 2% helix, 61% strand | P16009, G9IA38 |
| C | Chimera of bacteriophage obp GP146 and a T4 GP5 (EC 3.2.1.17) | protein | 146 | 2% helix, 61% strand | P16009, G9IA38 |
Ligands and binding sites
- STE · Stearic acid · ligand · 2 copies · chains A, B, C, D, E, F
- ELA · 9-octadecenoic acid · ligand · 2 copies · chains A, B, C, D, E, F
- PLM · Palmitic acid · ligand · 2 copies · chains A, B, C, D, E, F
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.86 | 0.86 | 73 | STE, ELA, PLM |
| 2 | 1026 | 0.85 | 0.85 | 74 | STE, ELA, PLM |
| 3 | 192 | 0.84 | 0.98 | 30 | MG |
| 4 | 185 | 0.84 | 0.98 | 30 | MG |
| 5 | 956 | 0.75 | 0.79 | 101 | empty |
Interfaces
13 interfaces between chains.
- D–E · 6236 Ų buried · 176 hydrogen bonds · protein-protein
- D–F · 6178 Ų buried · 178 hydrogen bonds · protein-protein
- E–F · 6165 Ų buried · 179 hydrogen bonds · protein-protein
- B–C · 6153 Ų buried · 176 hydrogen bonds · protein-protein
- A–B · 6152 Ų buried · 173 hydrogen bonds · protein-protein
Compared structures
- 6P2A · Chimera of bacteriophage OBP gp146 central spike protein and a T4 gp5 beta-helix fragment · 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 P16009
- Every structure of UniProt G9IA38
- Elsewhere: RCSB PDB 6P2A · PDBe 6P2A · UniProt P16009 · UniProt G9IA38
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