MolNFT v1 · #40442 · protein
Structure of the plp synthase holoenzyme from thermotoga maritima
2ISS · Pyridoxal biosynthesis lyase pdxs: “Structure of the plp synthase holoenzyme from thermotoga maritima”. X-ray diffraction, 2 ligands (5RP, PO4), 14 pockets (best druggability 0.71). MolNFT v1 #40442 on GenesisL1: 3D structure…
- PDB
- 2ISS
- Type
- protein
- Length
- 1,399 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal biosynthesis lyase pdxs; Glutamine amidotransferase subunit pdxt
- EC
- 4.-.-.-, 2.6.-.-
- UniProt
- Q9WYU4, Q9WYU3
- Ligands
- 5RP, PO4
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 281 | 46% helix, 14% strand | Q9WYU4 |
| B | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 285 | 45% helix, 14% strand | Q9WYU4 |
| C | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 280 | 45% helix, 14% strand | Q9WYU4 |
| D | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 185 | 31% helix, 32% strand | Q9WYU3 |
| E, F | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 184 | 31% helix, 33% strand | Q9WYU3 |
Ligands and binding sites
- 5RP · Ribulose-5-phosphate · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.71 | 0.98 | 18 | empty |
| 2 | 50 | 0.70 | 0.98 | 18 | empty |
| 3 | 228 | 0.65 | 0.83 | 33 | empty |
| 4 | 251 | 0.65 | 0.83 | 33 | empty |
| 5 | 126 | 0.65 | 0.88 | 29 | 5RP |
Interfaces
5 interfaces between chains.
- B–E · 2026 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1825 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1800 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1021 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1021 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 2ISS · Structure of the PLP synthase Holoenzyme from Thermotoga maritima · the same entry in another collection · chain F against F, TM-score 1.00
- Q9WYU4 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit pdxs… · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q9WYU3 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit pdxt… · a predicted model of the same protein · chain E against A, TM-score 0.98
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 Q9WYU4
- Every structure of UniProt Q9WYU3
- Elsewhere: RCSB PDB 2ISS · PDBe 2ISS · UniProt Q9WYU4 · UniProt Q9WYU3
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