Research workbench
Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (arabidopsis thaliana)
Analyse Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (arabidopsis thaliana) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LB5
- Type
- protein
- Length
- 3,120 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
- UniProt
- Q9ZNR6
- Pockets
- 20 · best druggability 0.68
Structure
electron microscopy · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | protein | 260 | 46% helix, 15% strand | Q9ZNR6 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.68 | 0.89 | 32 | empty |
| 2 | 130 | 0.68 | 0.90 | 33 | empty |
| 3 | 146 | 0.68 | 0.88 | 33 | empty |
| 4 | 123 | 0.66 | 0.89 | 31 | empty |
| 5 | 180 | 0.66 | 0.85 | 42 | empty |
Interfaces
24 interfaces between chains.
- C–J · 919 Ų buried · 5 hydrogen bonds · protein-protein
- D–I · 912 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 912 Ų buried · 5 hydrogen bonds · protein-protein
- B–K · 908 Ų buried · 5 hydrogen bonds · protein-protein
- E–H · 906 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7LB5 · Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (Arabidopsis thaliana) · the same entry in another collection · chain L against L, 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 Q9ZNR6
- Elsewhere: RCSB PDB 7LB5 · PDBe 7LB5 · UniProt Q9ZNR6
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