MolNFT v1 · #159859 · protein
Crystal structure of ligu
6P3J · (4E)-oxalomesaconate delta-isomerase: “Crystal structure of ligu”. X-ray diffraction, 3 ligands (CA, NA, CL), 6 pockets (best druggability 0.70). MolNFT v1 #159859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P3J
- Type
- protein
- Length
- 705 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (4E)-oxalomesaconate delta-isomerase
- EC
- 5.3.3.-
- UniProt
- Q0KJL4
- Ligands
- CA, NA, CL
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (4E)-oxalomesaconate delta-isomerase (EC 5.3.3.-) | protein | 353 | 19% helix, 35% strand | Q0KJL4 |
| B | (4E)-oxalomesaconate delta-isomerase (EC 5.3.3.-) | protein | 352 | 18% helix, 35% strand | Q0KJL4 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.70 | 0.81 | 50 | CL |
| 2 | 502 | 0.67 | 0.78 | 53 | CL |
| 3 | 152 | 0.46 | 0.76 | 25 | empty |
| 4 | 104 | 0.38 | 0.75 | 21 | empty |
| 5 | 56 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1711 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
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 Q0KJL4
- Elsewhere: RCSB PDB 6P3J · PDBe 6P3J · UniProt Q0KJL4
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