MolNFT v1 · #151797 · protein
PDX1.2/PDX1.3 complex (PDX1.3:K97A)
6HYE · Pyridoxal 5'-phosphate synthase-like subunit PDX1.2: “PDX1.2/PDX1.3 complex (PDX1.3:K97A)”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.79). MolNFT v1 #151797 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HYE
- Type
- protein
- Length
- 2,091 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 | 13% helix, 82% strand | Q9ZNR6 |
| C | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | protein | 261 | 20% helix, 74% strand | Q9ZNR6 |
| E | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | protein | 258 | 14% helix, 80% strand | Q9ZNR6 |
| G | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | protein | 262 | 16% helix, 78% strand | Q9ZNR6 |
| B | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 268 | 28% helix, 65% strand | Q8L940 |
| D | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 260 | 26% helix, 68% strand | Q8L940 |
| F | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 257 | 21% helix, 72% strand | Q8L940 |
| H | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 261 | 22% helix, 72% 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 | 791 | 0.79 | 0.82 | 181 | empty |
| 2 | 89 | 0.77 | 0.98 | 57 | SO4 |
| 3 | 443 | 0.71 | 0.81 | 120 | SO4 |
| 4 | 153 | 0.61 | 0.84 | 55 | empty |
| 5 | 144 | 0.54 | 0.81 | 63 | SO4 |
Interfaces
18 interfaces between chains.
- A–B · 5894 Ų buried · 1,977 hydrogen bonds · protein-protein
- G–H · 5887 Ų buried · 2,018 hydrogen bonds · protein-protein
- E–F · 5858 Ų buried · 1,910 hydrogen bonds · protein-protein
- C–D · 5844 Ų buried · 1,960 hydrogen bonds · protein-protein
- E–D · 946 Ų buried · 7 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 6HYE · PDBe 6HYE · UniProt Q9ZNR6 · UniProt Q8L940
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