Research workbench
Crystal structure of the D38A mutant of isochorismatase phzd from pseudomonas fluorescens 2-79 in complex with 2-amino-2- desoxyisochorismate adic
Analyse Crystal structure of the D38A mutant of isochorismatase phzd from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R77
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable isochorismatase
- EC
- 3.3.2.1
- UniProt
- Q51790
- Ligands
- QLI, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable isochorismatase (EC 3.3.2.1) | protein | 205 | 40% helix, 18% strand | Q51790 |
| B | Probable isochorismatase (EC 3.3.2.1) | protein | 206 | 40% helix, 17% strand | Q51790 |
Ligands and binding sites
- QLI · (5S,6S)-6-amino-5-[(1-carboxyethenyl)oxy]cyclohexa-1,3-diene-1-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.76 | 0.99 | 21 | QLI |
| 2 | 69 | 0.75 | 0.99 | 21 | QLI |
| 3 | 141 | 0.51 | 0.79 | 22 | empty |
| 4 | 61 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1418 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3R77 · Crystal structure of the D38A mutant of isochorismatase PhzD from Pseudomonas fluorescens… · the same entry in another collection · chain A against A, TM-score 1.00
- Q51790 · AlphaFold monomer V2.0 prediction for phenazine biosynthesis protein phzd (Q51790) · a predicted model of the same protein · chain A against A, 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 Q51790
- Elsewhere: RCSB PDB 3R77 · PDBe 3R77 · UniProt Q51790
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