MolNFT v1 · #137937 · protein
Crystal structure of POPP2 in complex with IP6
5W3T · POPP2 protein: “Crystal structure of POPP2 in complex with IP6”. X-ray diffraction, 1 ligand (IHP), 16 pockets (best druggability 0.73). MolNFT v1 #137937 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W3T
- Type
- protein
- Length
- 1,330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POPP2 protein
- UniProt
- A0A0S4VB05
- Ligands
- IHP
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POPP2 protein | protein | 332 | 48% helix, 20% strand | A0A0S4VB05 |
| B | POPP2 protein | protein | 333 | 48% helix, 20% strand | A0A0S4VB05 |
| C | POPP2 protein | protein | 332 | 49% helix, 19% strand | A0A0S4VB05 |
| D | POPP2 protein | protein | 333 | 48% helix, 20% strand | A0A0S4VB05 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.73 | 0.79 | 75 | IHP, GOL |
| 2 | 396 | 0.68 | 0.81 | 64 | empty |
| 3 | 133 | 0.59 | 0.84 | 29 | empty |
| 4 | 172 | 0.59 | 0.82 | 31 | empty |
| 5 | 147 | 0.57 | 0.82 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 480 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 455 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 423 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5W3T · Crystal structure of PopP2 in complex with IP6 · 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 5W3T · PDBe 5W3T · UniProt A0A0S4VB05
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