MolNFT v1 · #46125 · protein
Structure of the synthase subunit PDX1 (yaad) of plp synthase from bacillus subtilis
2NV1 · Pyridoxal biosynthesis lyase pdxs: “Structure of the synthase subunit PDX1 (yaad) of plp synthase from bacillus subtilis”. X-ray diffraction, 2 ligands (MG, CL), 13 pockets (best druggability 0.75). MolNFT v1 #46125 on GenesisL1: 3D…
- 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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