Research workbench
Crystal structure of POPP2 C321A in complex with IP6 and accoa
Analyse Crystal structure of POPP2 C321A 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
- 5W3Y
- Type
- protein
- Length
- 1,332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POPP2 protein
- UniProt
- A0A0S4VB05
- Ligands
- IHP, ACO
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POPP2 protein | protein | 336 | 48% helix, 20% strand | A0A0S4VB05 |
| B | POPP2 protein | protein | 327 | 46% helix, 18% strand | A0A0S4VB05 |
| C | POPP2 protein | protein | 335 | 48% helix, 20% strand | A0A0S4VB05 |
| D | POPP2 protein | protein | 334 | 48% helix, 20% strand | A0A0S4VB05 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 4 copies · chains A, B, C, D
- ACO · Acetyl coenzyme *A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.74 | 0.79 | 96 | IHP, ACO |
| 2 | 818 | 0.74 | 0.79 | 93 | ACO, IHP |
| 3 | 764 | 0.73 | 0.79 | 76 | IHP |
| 4 | 706 | 0.72 | 0.79 | 75 | IHP |
| 5 | 275 | 0.64 | 0.82 | 37 | empty |
Interfaces
6 interfaces between chains.
- C–D · 477 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 463 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 428 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5W3Y · Crystal structure of PopP2 C321A 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 5W3Y · PDBe 5W3Y · UniProt A0A0S4VB05
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