MolNFT v1 · #122061 · protein
Crystal structure of a plant enzyme
5IE3 · Oxalate--CoA ligase: “Crystal structure of a plant enzyme”. X-ray diffraction, 2 ligands (AMP, OXD), 12 pockets (best druggability 0.83). MolNFT v1 #122061 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IE3
- Type
- protein
- Length
- 1,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxalate--CoA ligase
- EC
- 6.2.1.8
- UniProt
- Q9SMT7
- Ligands
- AMP, OXD
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxalate--CoA ligase (EC 6.2.1.8) | protein | 504 | 33% helix, 27% strand | Q9SMT7 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- OXD · Oxalic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.83 | 0.84 | 107 | AMP, OXD |
| 2 | 915 | 0.82 | 0.84 | 109 | AMP, OXD |
| 3 | 513 | 0.70 | 0.80 | 77 | empty |
| 4 | 76 | 0.62 | 0.90 | 21 | empty |
| 5 | 219 | 0.60 | 0.81 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 820 Ų buried · 16 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 Q9SMT7
- Elsewhere: RCSB PDB 5IE3 · PDBe 5IE3 · UniProt Q9SMT7
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