Research workbench
1.37 ångström crystal structure of E. COLI 2-succinyl-6-hydroxy-2,4- cyclohexadiene-1-carboxylate synthase (menh) in complex with shchc
Analyse 1.37 ångström crystal structure of E. COLI 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
- 4MYD
- Type
- protein
- Length
- 754 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
- Pockets
- 6 · best druggability 0.74
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 | 46% helix, 15% strand | P37355 |
| C | 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20) | protein | 250 | 46% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.74 | 0.89 | 32 | empty |
| 2 | 220 | 0.72 | 0.87 | 32 | 164 |
| 3 | 261 | 0.69 | 0.84 | 33 | 164 |
| 4 | 383 | 0.59 | 0.76 | 74 | empty |
| 5 | 273 | 0.52 | 0.75 | 45 | empty |
Interfaces
2 interfaces between chains.
- A–C · 619 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4MYD · 1.37 Angstrom Crystal Structure of E. Coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carbo… · 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 C 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 4MYD · PDBe 4MYD · UniProt P37355
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.