Research workbench
1.4 ångström crystal structure of 2-succinyl-6-hydroxy-2,4- cyclohexadiene-1-carboxylate synthase with shchc and pyruvate
Analyse 1.4 ångström crystal structure of 2-succinyl-6-hydroxy-2,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MYS
- Type
- protein
- Length
- 755 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
- EC
- 4.2.99.20
- UniProt
- P37355
- Ligands
- 164, PYR
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20) | protein | 252 | 47% helix, 15% strand | P37355 |
| C | 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20) | protein | 251 | 45% helix, 15% strand | P37355 |
Ligands and binding sites
- 164 · 2-(3-carboxypropionyl)-6-hydroxy-cyclohexa-2,4-diene carboxylic acid · ligand · 2 copies · chains A, B
- PYR · Pyruvic acid · ligand · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.75 | 0.92 | 32 | empty |
| 2 | 258 | 0.70 | 0.85 | 33 | 164, GOL |
| 3 | 277 | 0.68 | 0.83 | 39 | 164, PYR |
| 4 | 290 | 0.58 | 0.77 | 50 | empty |
| 5 | 93 | 0.53 | 0.84 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 633 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 369 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4MYS · 1.4 Angstrom Crystal Structure of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate… · the same entry in another collection · chain A against A, TM-score 1.00
- P37355 · AlphaFold monomer V2.0 prediction for 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylat… · 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 P37355
- Elsewhere: RCSB PDB 4MYS · PDBe 4MYS · UniProt P37355
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