Research workbench
Crystal structure of tryptophan synthase alpha chain homolog BX1: a member of the chemical plant defense system
Analyse Crystal structure of tryptophan synthase alpha chain homolog BX1: a member of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RD5
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain, chloroplast
- EC
- 4.2.1.20
- UniProt
- P42390
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain, chloroplast (EC 4.2.1.20) | protein | 261 | 48% helix, 15% strand | P42390 |
| B | Tryptophan synthase alpha chain, chloroplast (EC 4.2.1.20) | protein | 248 | 52% helix, 15% strand | P42390 |
Ligands and binding sites
- MLA · Malonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.69 | 0.81 | 52 | empty |
| 2 | 186 | 0.66 | 0.85 | 29 | empty |
| 3 | 284 | 0.64 | 0.80 | 37 | MLA |
| 4 | 149 | 0.62 | 0.84 | 19 | MLA |
| 5 | 174 | 0.55 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1039 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1RD5 · Crystal structure of Tryptophan synthase alpha chain homolog BX1: a member of the… · the same entry in another collection · chain A against A, TM-score 1.00
- P42390 · AlphaFold monomer V2.0 prediction for indole-3-glycerol phosphate lyase, chloroplastic… · a predicted model of the same protein · chain B 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 P42390
- Elsewhere: RCSB PDB 1RD5 · PDBe 1RD5 · UniProt P42390
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