Research workbench
Crystal structure of dipeptide epimerase from methylococcus capsulatus complexed with mg ion
Analyse Crystal structure of dipeptide epimerase from methylococcus capsulatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RO6
- Type
- protein
- Length
- 2,067 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative chloromuconate cycloisomerase
- UniProt
- Q607C7
- Ligands
- MG, SO4
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E, F | Putative chloromuconate cycloisomerase | protein | 344 | 41% helix, 23% strand | Q607C7 |
| A | Putative chloromuconate cycloisomerase | protein | 345 | 40% helix, 23% strand | Q607C7 |
| C | Putative chloromuconate cycloisomerase | protein | 346 | 42% helix, 23% strand | Q607C7 |
| D | Putative chloromuconate cycloisomerase | protein | 344 | 42% helix, 22% strand | Q607C7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains B, A, C, D, E, F
- SO4 · Sulfate ion · ion · 13 copies · chains B, A, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.84 | 0.85 | 78 | empty |
| 2 | 926 | 0.83 | 0.85 | 85 | empty |
| 3 | 857 | 0.68 | 0.74 | 87 | GOL |
| 4 | 445 | 0.58 | 0.75 | 41 | SO4 |
| 5 | 299 | 0.58 | 0.77 | 38 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1289 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1271 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 260 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 208 Ų buried · 2 hydrogen bonds · protein-protein
- B–A · 167 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3RO6 · Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg… · the same entry in another collection · chain F against F, TM-score 1.00
- Q607C7 · AlphaFold monomer V2.0 prediction for L-lys-D/L-arg epimerase (Q607C7) · a predicted model of the same protein · chain D 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 Q607C7
- Elsewhere: RCSB PDB 3RO6 · PDBe 3RO6 · UniProt Q607C7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.