Research workbench
Crystal structure of bifunctional indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpc) from corynebacterium glutamicum in complex with reduced 1-(O-carboxyphenylamino)-1- deoxyribulose 5-phosphate (rcdrp)
Analyse Crystal structure of bifunctional indole-3-glycerol phosphate synthase /… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ETY
- Type
- protein
- Length
- 931 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan biosynthesis protein trpcf
- EC
- 4.1.1.48, 5.3.1.24
- UniProt
- P06560
- Ligands
- 137
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan biosynthesis protein trpcf (EC 4.1.1.48, 5.3.1.24) | protein | 470 | 41% helix, 19% strand | P06560 |
| B | Tryptophan biosynthesis protein trpcf (EC 4.1.1.48, 5.3.1.24) | protein | 461 | 41% helix, 18% strand | P06560 |
Ligands and binding sites
- 137 · 1-(O-carboxy-phenylamino)-1-deoxy-D-ribulose-5-phosphate · ligand · 4 copies · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.79 | 0.96 | 29 | 137 |
| 2 | 153 | 0.79 | 0.95 | 31 | 137 |
| 3 | 1039 | 0.73 | 0.76 | 99 | GOL |
| 4 | 102 | 0.68 | 0.92 | 30 | 137 |
| 5 | 265 | 0.52 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1985 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7ETY · Crystal structure of bifunctional indole-3-glycerol phosphate synthase /… · the same entry in another collection · chain A against A, TM-score 1.00
- P06560 · AlphaFold monomer V2.0 prediction for tryptophan biosynthesis protein trpcf (P06560) · a predicted model of the same protein · chain A 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 P06560
- Elsewhere: RCSB PDB 7ETY · PDBe 7ETY · UniProt P06560
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