Research workbench
Azobenzene-based inhibitors for tryptophan synthase
Analyse Azobenzene-based inhibitors for tryptophan synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A20
- Type
- protein
- Length
- 1,289 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha CHAIN,TRYPTOPHAN synthase beta chain
- EC
- 4.2.1.20
- UniProt
- A0A0D6FWC1, A0A0F7J6T4
- Ligands
- NA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha CHAIN,TRYPTOPHAN synthase beta chain (EC 4.2.1.20) | protein | 256 | 52% helix, 14% strand | A0A0D6FWC1 |
| B | Tryptophan synthase alpha CHAIN,TRYPTOPHAN synthase beta chain (EC 4.2.1.20) | protein | 390 | 45% helix, 20% strand | A0A0F7J6T4 |
| C | Tryptophan synthase alpha CHAIN,TRYPTOPHAN synthase beta chain (EC 4.2.1.20) | protein | 249 | 49% helix, 14% strand | A0A0D6FWC1 |
| D | Tryptophan synthase alpha CHAIN,TRYPTOPHAN synthase beta chain (EC 4.2.1.20) | protein | 394 | 46% helix, 19% strand | A0A0F7J6T4 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, D
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.83 | 0.84 | 113 | 144 |
| 2 | 1185 | 0.82 | 0.84 | 124 | 144 |
| 3 | 425 | 0.77 | 0.85 | 59 | empty |
| 4 | 334 | 0.69 | 0.82 | 37 | empty |
| 5 | 197 | 0.59 | 0.81 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1354 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1344 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 347 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 266 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 239 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7A20 · Azobenzene-Based Inhibitors for Tryptophan Synthase · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A0D6FWC1
- Every structure of UniProt A0A0F7J6T4
- Elsewhere: RCSB PDB 7A20 · PDBe 7A20 · UniProt A0A0D6FWC1 · UniProt A0A0F7J6T4
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