MolNFT v1 · #116071 · protein
4-oxalocrotonate decarboxylase from pseudomonas putida G7 - complexed with calcium and acetate
5D2I · 4-oxalocrotonate decarboxylase nahk: “4-oxalocrotonate decarboxylase from pseudomonas putida G7 - complexed with calcium and acetate”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.76). MolNFT v1 #116071 on…
- PDB
- 5D2I
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-oxalocrotonate decarboxylase nahk
- EC
- 4.1.1.77
- UniProt
- Q1XGK3
- Ligands
- CA
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-oxalocrotonate decarboxylase nahk (EC 4.1.1.77) | protein | 263 | 32% helix, 30% strand | Q1XGK3 |
| B | 4-oxalocrotonate decarboxylase nahk (EC 4.1.1.77) | protein | 259 | 32% helix, 31% strand | Q1XGK3 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.76 | 0.84 | 47 | CA, EDO, ACT |
| 2 | 174 | 0.54 | 0.79 | 29 | CA, ACT |
| 3 | 199 | 0.45 | 0.74 | 28 | EDO |
| 4 | 74 | 0.35 | 0.76 | 20 | empty |
| 5 | 52 | 0.32 | 0.77 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 585 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5D2I · 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with calcium and… · 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 Q1XGK3
- Elsewhere: RCSB PDB 5D2I · PDBe 5D2I · UniProt Q1XGK3
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