MolNFT v1 · #142998 · protein
Engineered tryptophan synthase B-subunit from pyrococcus furiosus, PFTRPB2B9 with TRP bound as E(AEX2)
6AM8 · Tryptophan synthase beta chain 1: “Engineered tryptophan synthase B-subunit from pyrococcus furiosus, PFTRPB2B9 with TRP bound as E(AEX2)”. X-ray diffraction, 3 ligands (TRP, PLT, NA), 16 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 6AM8
- Type
- protein
- Length
- 1,533 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase beta chain 1
- EC
- 4.2.1.20
- UniProt
- Q8U093
- Ligands
- TRP, PLT, NA
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 384 | 48% helix, 22% strand | Q8U093 |
| B | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 385 | 49% helix, 21% strand | Q8U093 |
| C | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 387 | 48% helix, 20% strand | Q8U093 |
| D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 377 | 49% helix, 20% strand | Q8U093 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 3 copies · chains A, B, D
- PLT · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-L-tryptophane · ligand · 2 copies · chains B, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.82 | 0.98 | 35 | PLT |
| 2 | 130 | 0.80 | 0.98 | 35 | PLT |
| 3 | 88 | 0.75 | 0.98 | 31 | empty |
| 4 | 77 | 0.74 | 0.98 | 32 | empty |
| 5 | 80 | 0.74 | 0.97 | 18 | TRP |
Interfaces
5 interfaces between chains.
- A–B · 1761 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1751 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 124 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 6AM8 · Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9 with Trp… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8U093 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain 1 (Q8U093) · a predicted model of the same protein · chain D 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 Q8U093
- Elsewhere: RCSB PDB 6AM8 · PDBe 6AM8 · UniProt Q8U093
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.