MolNFT v1 · #151764 · protein
PDX1.2/PDX1.3 complex (intermediate)
6HXG · Pyridoxal 5'-phosphate synthase-like subunit PDX1.2: “PDX1.2/PDX1.3 complex (intermediate)”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.79). MolNFT v1 #151764 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HXG
- Type
- protein
- Length
- 2,078 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal 5'-phosphate synthase-like subunit PDX1.2; Pyridoxal 5'-phosphate synthase…
- EC
- 4.3.3.6
- UniProt
- Q9ZNR6, Q8L940
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 20% helix, 74% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | protein | 264 | 20% helix, 74% strand | Q9ZNR6 |
| C | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | protein | 259 | 21% helix, 73% strand | Q9ZNR6 |
| E | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | protein | 255 | 17% helix, 77% strand | Q9ZNR6 |
| G | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | protein | 260 | 13% helix, 82% strand | Q9ZNR6 |
| B | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 269 | 22% helix, 73% strand | Q8L940 |
| D | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 258 | 19% helix, 74% strand | Q8L940 |
| F | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 254 | 26% helix, 69% strand | Q8L940 |
| H | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 259 | 25% helix, 69% strand | Q8L940 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.79 | 0.82 | 194 | empty |
| 2 | 144 | 0.62 | 0.86 | 56 | empty |
| 3 | 280 | 0.57 | 0.77 | 80 | SO4 |
| 4 | 128 | 0.57 | 0.84 | 54 | empty |
| 5 | 192 | 0.54 | 0.79 | 69 | SO4 |
Interfaces
20 interfaces between chains.
- A–B · 5876 Ų buried · 1,915 hydrogen bonds · protein-protein
- G–H · 5805 Ų buried · 1,899 hydrogen bonds · protein-protein
- C–D · 5805 Ų buried · 1,879 hydrogen bonds · protein-protein
- E–F · 5767 Ų buried · 1,863 hydrogen bonds · protein-protein
- G–B · 952 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
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 Q9ZNR6
- Every structure of UniProt Q8L940
- Elsewhere: RCSB PDB 6HXG · PDBe 6HXG · UniProt Q9ZNR6 · UniProt Q8L940
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