Research workbench
Pyruvate-bound structure of the isochorismate-pyruvate lyase from pseudomonas aerugionsa
Analyse Pyruvate-bound structure of the isochorismate-pyruvate lyase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H9D
- Type
- protein
- Length
- 369 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Salicylate biosynthesis protein pchb
- EC
- 4.1.99.-
- UniProt
- Q51507
- Ligands
- PYR, CA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Salicylate biosynthesis protein pchb (EC 4.1.99.-) | protein | 84 | 79% helix, 0% strand | Q51507 |
| B | Salicylate biosynthesis protein pchb (EC 4.1.99.-) | protein | 87 | 80% helix, 0% strand | Q51507 |
| C | Salicylate biosynthesis protein pchb (EC 4.1.99.-) | protein | 98 | 77% helix, 0% strand | Q51507 |
| D | Salicylate biosynthesis protein pchb (EC 4.1.99.-) | protein | 100 | 81% helix, 0% strand | Q51507 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.77 | 0.97 | 19 | PYR |
| 2 | 97 | 0.75 | 0.96 | 18 | PYR |
| 3 | 100 | 0.65 | 0.89 | 21 | PYR |
| 4 | 140 | 0.56 | 0.82 | 17 | PYR |
| 5 | 107 | 0.42 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2478 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2395 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 555 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 283 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2H9D · Pyruvate-Bound Structure of the Isochorismate-Pyruvate Lyase from Pseudomonas aerugionsa · the same entry in another collection · chain D against D, TM-score 1.00
- Q51507 · AlphaFold monomer V2.0 prediction for isochorismate pyruvate lyase (Q51507) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q51507
- Elsewhere: RCSB PDB 2H9D · PDBe 2H9D · UniProt Q51507
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