MolNFT v1 · #159857 · protein
Crystal structure of LIGU(K66M) bound to substrate
6P3H · (4E)-oxalomesaconate delta-isomerase: “Crystal structure of LIGU(K66M) bound to substrate”. X-ray diffraction, 2 ligands (NQM, CL), 10 pockets (best druggability 0.73). MolNFT v1 #159857 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6P3H
- Type
- protein
- Length
- 1,405 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (4E)-oxalomesaconate delta-isomerase
- EC
- 5.3.3.-
- UniProt
- Q0KJL4
- Ligands
- NQM, CL
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B | (4E)-oxalomesaconate delta-isomerase (EC 5.3.3.-) | protein | 351 | 21% helix, 35% strand | Q0KJL4 |
| C | (4E)-oxalomesaconate delta-isomerase (EC 5.3.3.-) | protein | 352 | 20% helix, 34% strand | Q0KJL4 |
Ligands and binding sites
- NQM · (1E)-4-oxobut-1-ene-1,2,4-tricarboxylic acid · ligand · 4 copies · chains A, D, C, B
- CL · Chloride ion · ion · 6 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.73 | 0.98 | 22 | NQM |
| 2 | 581 | 0.73 | 0.80 | 73 | NQM |
| 3 | 53 | 0.72 | 0.99 | 19 | NQM |
| 4 | 53 | 0.71 | 0.98 | 19 | NQM |
| 5 | 603 | 0.69 | 0.78 | 67 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1554 Ų buried · 29 hydrogen bonds · protein-protein
- D–B · 1549 Ų buried · 30 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 6P3H · PDBe 6P3H · UniProt Q0KJL4
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