Research workbench
Crystal structure of 4-methylmuconolactone methylisomerase in complex with mes
Analyse Crystal structure of 4-methylmuconolactone methylisomerase in complex with mes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HDS
- Type
- protein
- Length
- 459 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-methylmuconolactone methylisomerase; Short peptide aswsa
- EC
- 5.4.99.14
- UniProt
- C5MR76
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-methylmuconolactone methylisomerase (EC 5.4.99.14) | protein | 116 | 38% helix, 28% strand | C5MR76 |
| B | 4-methylmuconolactone methylisomerase (EC 5.4.99.14) | protein | 115 | 37% helix, 29% strand | C5MR76 |
| C, D | 4-methylmuconolactone methylisomerase (EC 5.4.99.14) | protein | 109 | 33% helix, 31% strand | C5MR76 |
| E, F | Short peptide aswsa | protein | 5 | 0% helix, 60% strand | — |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.73 | 0.89 | 24 | MES |
| 2 | 184 | 0.72 | 0.89 | 26 | MES |
| 3 | 162 | 0.72 | 0.89 | 27 | MES |
| 4 | 160 | 0.67 | 0.87 | 25 | MES |
| 5 | 301 | 0.59 | 0.78 | 42 | empty |
Interfaces
9 interfaces between chains.
- A–D · 2254 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2192 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 362 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 356 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 205 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3HDS · Crystal structure of 4-methylmuconolactone methylisomerase in complex with MES · the same entry in another collection · 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 C5MR76
- Elsewhere: RCSB PDB 3HDS · PDBe 3HDS · UniProt C5MR76
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