Research workbench
Crystal structure of hpcg complexed with mg ion
Analyse Crystal structure of hpcg complexed with mg ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EB6
- Type
- protein
- Length
- 1,334 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxo-hept-3-ene-1,7-dioate hydratase
- EC
- 4.2.1.-
- UniProt
- Q46982
- Ligands
- MG
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 267 | 33% helix, 31% strand | Q46982 |
| D | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 266 | 33% helix, 32% strand | Q46982 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.69 | 0.79 | 46 | empty |
| 2 | 511 | 0.68 | 0.79 | 44 | empty |
| 3 | 549 | 0.68 | 0.78 | 47 | empty |
| 4 | 520 | 0.68 | 0.78 | 44 | empty |
| 5 | 509 | 0.67 | 0.78 | 45 | empty |
Interfaces
5 interfaces between chains.
- B–C · 593 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 573 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 570 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 564 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 561 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2EB6 · Crystal structure of HpcG complexed with Mg ion · 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 Q46982
- Elsewhere: RCSB PDB 2EB6 · PDBe 2EB6 · UniProt Q46982
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