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Engineered tryptophan synthase B-subunit from pyrococcus furiosus, PFTRPB4D11 with TRP non-covalently bound
Analyse Engineered tryptophan synthase B-subunit from pyrococcus furiosus, PFTRPB4D11… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AMI
- Type
- protein
- Length
- 1,539 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, NA
- Pockets
- 18 · best druggability 0.77
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 | 383 | 50% helix, 21% strand | Q8U093 |
| B | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 387 | 49% helix, 21% strand | Q8U093 |
| C | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 385 | 49% helix, 21% strand | Q8U093 |
| D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 384 | 49% helix, 20% strand | Q8U093 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.77 | 0.82 | 69 | empty |
| 2 | 102 | 0.77 | 0.97 | 24 | TRP |
| 3 | 96 | 0.76 | 0.97 | 31 | empty |
| 4 | 94 | 0.76 | 0.97 | 28 | empty |
| 5 | 82 | 0.75 | 0.97 | 19 | TRP |
Interfaces
5 interfaces between chains.
- A–B · 1895 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1780 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 190 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 79 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6AMI · Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11 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 B 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 6AMI · PDBe 6AMI · UniProt Q8U093
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