MolNFT v1 · #135654 · protein
PSF3 in complex with NADP+ and 2-opp
5U5G · 6-phosphogluconate dehydrogenase: “PSF3 in complex with NADP+ and 2-opp”. X-ray diffraction, 2 ligands (NAP, 7VD), 9 pockets (best druggability 0.74). MolNFT v1 #135654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U5G
- Type
- protein
- Length
- 1,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase
- UniProt
- I6R485
- Ligands
- NAP, 7VD
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase | protein | 286 | 57% helix, 14% strand | I6R485 |
| B, D | 6-phosphogluconate dehydrogenase | protein | 284 | 56% helix, 14% strand | I6R485 |
| C | 6-phosphogluconate dehydrogenase | protein | 283 | 57% helix, 14% strand | I6R485 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 7VD · (2-oxopropyl)phosphonic acid · ligand · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.74 | 0.85 | 50 | NAP, 7VD |
| 2 | 336 | 0.73 | 0.86 | 41 | NAP, 7VD |
| 3 | 382 | 0.73 | 0.84 | 49 | NAP, 7VD |
| 4 | 348 | 0.72 | 0.84 | 39 | NAP, 7VD |
| 5 | 88 | 0.35 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2655 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2610 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 161 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U5G · Psf3 in complex with NADP+ and 2-OPP · 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 I6R485
- Elsewhere: RCSB PDB 5U5G · PDBe 5U5G · UniProt I6R485
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