Research workbench
Crystal structure of hpcg complexed with oxalate
Analyse Crystal structure of hpcg complexed with oxalate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EB5
- Type
- protein
- Length
- 1,300 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
- OXL, MG, SCN
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 259 | 34% helix, 31% strand | Q46982 |
| B | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 263 | 33% helix, 32% strand | Q46982 |
| C | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 261 | 34% helix, 31% strand | Q46982 |
| E | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 258 | 34% helix, 31% strand | Q46982 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
- SCN · Thiocyanate ion · ion · 7 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 | 500 | 0.69 | 0.79 | 43 | empty |
| 2 | 500 | 0.69 | 0.79 | 42 | empty |
| 3 | 493 | 0.68 | 0.79 | 43 | empty |
| 4 | 504 | 0.68 | 0.78 | 42 | empty |
| 5 | 359 | 0.65 | 0.80 | 46 | MG, OXL |
Interfaces
5 interfaces between chains.
- B–C · 554 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 553 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 551 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 529 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2EB5 · Crystal structure of HpcG complexed with oxalate · 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 2EB5 · PDBe 2EB5 · UniProt Q46982
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