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Structure of the synthase subunit PDX1 (yaad) of plp synthase from bacillus subtilis
Analyse Structure of the synthase subunit PDX1 (yaad) of plp synthase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NV1
- Type
- protein
- Length
- 1,529 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal biosynthesis lyase pdxs
- EC
- 4.-.-.-
- UniProt
- P37527
- Ligands
- MG, CL
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 259 | 48% helix, 13% strand | P37527 |
| B | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 252 | 47% helix, 13% strand | P37527 |
| C | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 256 | 48% helix, 13% strand | P37527 |
| D | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 256 | 48% helix, 14% strand | P37527 |
| E | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 256 | 48% helix, 13% strand | P37527 |
| F | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 250 | 48% helix, 14% strand | P37527 |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, F, B, C, D, E
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.75 | 0.79 | 130 | CL, EDO |
| 2 | 493 | 0.68 | 0.79 | 71 | CL |
| 3 | 359 | 0.63 | 0.79 | 62 | CL |
| 4 | 169 | 0.58 | 0.81 | 30 | CL |
| 5 | 173 | 0.57 | 0.81 | 31 | CL |
Interfaces
6 interfaces between chains.
- B–C · 1003 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1003 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 998 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 997 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 993 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2NV1 · Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis · the same entry in another collection · chain F against F, TM-score 1.00
- P37527 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit pdxs… · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P37527
- Elsewhere: RCSB PDB 2NV1 · PDBe 2NV1 · UniProt P37527
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