Research workbench
Crystal structure of muconate lactonizing enzyme from ruegeria pomeroyi.
Analyse Crystal structure of muconate lactonizing enzyme from ruegeria pomeroyi. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I6E
- Type
- protein
- Length
- 2,848 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muconate cycloisomerase I
- EC
- 5.5.1.1
- UniProt
- Q5LM96
- Ligands
- MG, NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Muconate cycloisomerase I (EC 5.5.1.1) | protein | 356 | 42% helix, 21% strand | Q5LM96 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.88 | 0.90 | 118 | empty |
| 2 | 999 | 0.88 | 0.90 | 117 | empty |
| 3 | 998 | 0.88 | 0.90 | 115 | empty |
| 4 | 998 | 0.88 | 0.90 | 118 | empty |
| 5 | 293 | 0.64 | 0.81 | 44 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1254 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 1254 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 1224 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 1183 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1181 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3I6E · CRYSTAL STRUCTURE OF MUCONATE LACTONIZING ENZYME FROM Ruegeria pomeroyi. · 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 Q5LM96
- Elsewhere: RCSB PDB 3I6E · PDBe 3I6E · UniProt Q5LM96
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.