MolNFT v1 · #96424 · protein
Crystal structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase
4JJ9: “Crystal structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.83). MolNFT v1 #96424 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JJ9
- Type
- protein
- Length
- 448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-carboxymethyl-2-hydroxymuconate delta-isomerase
- EC
- 5.3.3.10
- UniProt
- Q7WPE6
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-carboxymethyl-2-hydroxymuconate delta-isomerase (EC 5.3.3.10) | protein | 152 | 38% helix, 28% strand | Q7WPE6 |
| B | 5-carboxymethyl-2-hydroxymuconate delta-isomerase (EC 5.3.3.10) | protein | 151 | 34% helix, 28% strand | Q7WPE6 |
| C | 5-carboxymethyl-2-hydroxymuconate delta-isomerase (EC 5.3.3.10) | protein | 145 | 37% helix, 29% strand | Q7WPE6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.83 | 0.88 | 39 | empty |
| 2 | 103 | 0.40 | 0.77 | 25 | SO4 |
| 3 | 78 | 0.39 | 0.78 | 18 | SO4 |
| 4 | 58 | 0.37 | 0.80 | 19 | SO4 |
| 5 | 57 | 0.30 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1632 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1619 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1582 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4JJ9 · Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase · 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 Q7WPE6
- Elsewhere: RCSB PDB 4JJ9 · PDBe 4JJ9 · UniProt Q7WPE6
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