Research workbench
Crystal structure of muconate lactonizing enzyme from mucobacterium smegmatis complexed with muconolactone
Analyse Crystal structure of muconate lactonizing enzyme from mucobacterium smegmatis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DG7
- Type
- protein
- Length
- 1,464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muconate cycloisomerase
- EC
- 5.5.1.-
- UniProt
- A0QTN8
- Ligands
- MUC, MG
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Muconate cycloisomerase (EC 5.5.1.-) | protein | 366 | 42% helix, 22% strand | A0QTN8 |
Ligands and binding sites
- MUC · [(2S)-5-oxo-2,5-dihydrofuran-2-yl]acetic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.87 | 0.90 | 107 | empty |
| 2 | 167 | 0.82 | 0.97 | 33 | empty |
| 3 | 161 | 0.82 | 0.97 | 34 | empty |
| 4 | 283 | 0.67 | 0.83 | 47 | empty |
| 5 | 297 | 0.66 | 0.82 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1234 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1198 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1198 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 550 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 550 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3DG7 · Crystal structure of muconate lactonizing enzyme from Mucobacterium Smegmatis complexed… · 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 A0QTN8
- Elsewhere: RCSB PDB 3DG7 · PDBe 3DG7 · UniProt A0QTN8
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