MolNFT v1 · #137167 · protein
Structure of oxalate decarboxylase from bacillus subtilis at pH 4.6
5VG3: “Structure of oxalate decarboxylase from bacillus subtilis at pH 4.6”. X-ray diffraction, 1 ligand (MN), 10 pockets (best druggability 0.52). MolNFT v1 #137167 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VG3
- Type
- protein
- Length
- 1,135 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxalate decarboxylase
- EC
- 4.1.1.2
- UniProt
- A0A162QMS4
- Ligands
- MN
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxalate decarboxylase (EC 4.1.1.2) | protein | 382 | 15% helix, 39% strand | A0A162QMS4 |
| B | Oxalate decarboxylase (EC 4.1.1.2) | protein | 376 | 15% helix, 40% strand | A0A162QMS4 |
| C | Oxalate decarboxylase (EC 4.1.1.2) | protein | 377 | 15% helix, 40% strand | A0A162QMS4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C
- ACT · Acetate ion · additive · 14 copies · chains A, C, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.52 | 0.74 | 34 | empty |
| 2 | 173 | 0.44 | 0.74 | 26 | empty |
| 3 | 134 | 0.43 | 0.75 | 21 | empty |
| 4 | 132 | 0.42 | 0.75 | 27 | ACT |
| 5 | 131 | 0.41 | 0.75 | 22 | ACT |
Interfaces
3 interfaces between chains.
- A–B · 2367 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 2310 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 2301 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5VG3 · Structure of Oxalate Decarboxylase from Bacillus subtilis at pH 4.6 · 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 A0A162QMS4
- Elsewhere: RCSB PDB 5VG3 · PDBe 5VG3 · UniProt A0A162QMS4
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