Research workbench
Crystal structure of POPP2 F318S in complex with IP6 and accoa
Analyse Crystal structure of POPP2 F318S in complex with IP6 and accoa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W40
- Type
- protein
- Length
- 1,329 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POPP2 protein
- UniProt
- A0A0S4VB05
- Ligands
- IHP, COA
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POPP2 protein | protein | 336 | 46% helix, 19% strand | A0A0S4VB05 |
| B | POPP2 protein | protein | 333 | 48% helix, 19% strand | A0A0S4VB05 |
| C | POPP2 protein | protein | 333 | 47% helix, 19% strand | A0A0S4VB05 |
| D | POPP2 protein | protein | 327 | 48% helix, 20% strand | A0A0S4VB05 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 4 copies · chains A, B, C, D
- COA · Coenzyme A · ligand · 4 copies · chains A, D, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.73 | 0.79 | 74 | IHP |
| 2 | 700 | 0.71 | 0.78 | 73 | IHP |
| 3 | 613 | 0.70 | 0.79 | 69 | IHP |
| 4 | 673 | 0.70 | 0.78 | 72 | IHP |
| 5 | 293 | 0.62 | 0.80 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–B · 503 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 456 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 440 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 421 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 5W40 · Crystal structure of PopP2 F318S in complex with IP6 and AcCoA · 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 A0A0S4VB05
- Elsewhere: RCSB PDB 5W40 · PDBe 5W40 · UniProt A0A0S4VB05
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