MolNFT v1 · #35426 · protein
Crystal structure of apo-hpcg
2EB4 · 2-oxo-hept-3-ene-1,7-dioate hydratase: “Crystal structure of apo-hpcg”. X-ray diffraction, 2 ligands (NA, SCN), 15 pockets (best druggability 0.72). MolNFT v1 #35426 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2EB4
- Type
- protein
- Length
- 1,309 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
- NA, SCN
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 261 | 34% helix, 30% strand | Q46982 |
| B | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 265 | 33% helix, 32% strand | Q46982 |
| C | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 262 | 34% helix, 31% strand | Q46982 |
| D | 2-oxo-hept-3-ene-1,7-dioate hydratase (EC 4.2.1.-) | protein | 260 | 34% helix, 30% strand | Q46982 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
- SCN · Thiocyanate ion · ion · 9 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.72 | 0.81 | 43 | SCN |
| 2 | 522 | 0.69 | 0.79 | 43 | empty |
| 3 | 514 | 0.68 | 0.79 | 47 | empty |
| 4 | 514 | 0.68 | 0.78 | 41 | empty |
| 5 | 470 | 0.66 | 0.78 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–E · 561 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 561 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 546 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 543 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 541 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2EB4 · Crystal structure of apo-HpcG · 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 2EB4 · PDBe 2EB4 · UniProt Q46982
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