Research workbench
Structure of the plp synthase complex PDX1/2 (YAAD/E) from bacillus subtilis
Analyse Structure of the plp synthase complex PDX1/2 (YAAD/E) from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NV2
- Type
- protein
- Length
- 5,554 residues
- Chains
- 24
- 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
- P37527, P37528
- Ligands
- GLN, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 10 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, O | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 268 | 49% helix, 14% strand | P37527 |
| B, H, N, P, R | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 193 | 31% helix, 31% strand | P37528 |
| C, E, M | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 269 | 48% helix, 13% strand | P37527 |
| D, T, V | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 194 | 31% helix, 31% strand | P37528 |
| F | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 191 | 31% helix, 31% strand | P37528 |
| I, U | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 271 | 48% helix, 14% strand | P37527 |
| J | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 196 | 33% helix, 31% strand | P37528 |
| K, Q, S, W | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 270 | 49% helix, 13% strand | P37527 |
| L | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 192 | 31% helix, 31% strand | P37528 |
| X | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 195 | 32% helix, 31% strand | P37528 |
Ligands and binding sites
- GLN · Glutamine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- CL · Chloride ion · ion · 12 copies · chains A, O, C, M, E, W, G, U, I, S, K, Q
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, O, C, M, E, W, G, U, I, S, K, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 479 | 0.74 | 0.83 | 63 | empty |
| 2 | 500 | 0.73 | 0.82 | 63 | empty |
| 3 | 527 | 0.73 | 0.81 | 67 | empty |
| 4 | 497 | 0.73 | 0.81 | 61 | empty |
| 5 | 437 | 0.72 | 0.82 | 61 | empty |
Interfaces
36 interfaces between chains.
- I–J · 1571 Ų buried · 33 hydrogen bonds · protein-protein
- W–X · 1560 Ų buried · 26 hydrogen bonds · protein-protein
- O–P · 1557 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1557 Ų buried · 25 hydrogen bonds · protein-protein
- M–N · 1553 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- P37528 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit pdxt… · a predicted model of the same protein · chain F 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
- Every structure of UniProt P37528
- Elsewhere: RCSB PDB 2NV2 · PDBe 2NV2 · UniProt P37527 · UniProt P37528
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