MolNFT v1 · #40651 · protein
Pex inhibitor-home data
2IZ0 · 6-phosphogluconate dehydrogenase, decarboxylating: “Pex inhibitor-home data”. X-ray diffraction, 4 ligands (ATR, NAP, RES), 14 pockets (best druggability 0.73). MolNFT v1 #40651 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2IZ0
- Type
- protein
- Length
- 1,406 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase, decarboxylating
- EC
- 1.1.1.44
- UniProt
- P96789
- Ligands
- ATR, NAP, RES, CL
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 469 | 56% helix, 10% strand | P96789 |
| B | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 469 | 57% helix, 10% strand | P96789 |
| C | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 468 | 56% helix, 9% strand | P96789 |
Ligands and binding sites
- ATR · 2'-monophosphoadenosine-5'-diphosphate · ligand · 2 copies · chains B, C
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, B
- RES · 4-phospho-D-erythronohydroxamic acid · ligand · chains A, B
- CL · Chloride ion · ion · 4 copies · chains B, C
- GOL · Glycerol · additive · 2 copies · chains A, C
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 2 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.73 | 0.98 | 25 | empty |
| 2 | 397 | 0.70 | 0.82 | 46 | NAP, RES |
| 3 | 503 | 0.63 | 0.76 | 31 | empty |
| 4 | 433 | 0.63 | 0.77 | 50 | CL |
| 5 | 409 | 0.55 | 0.74 | 67 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 6071 Ų buried · 76 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 P96789
- Elsewhere: RCSB PDB 2IZ0 · PDBe 2IZ0 · UniProt P96789
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