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A structural element that modulates proton-coupled electron transfer in oxalate decarboxylase
Analyse A structural element that modulates proton-coupled electron transfer in oxalate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S0M
- Type
- protein
- Length
- 377 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxalate decarboxylase oxdc
- EC
- 4.1.1.2
- UniProt
- O34714
- Ligands
- MN, CO3
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxalate decarboxylase oxdc (EC 4.1.1.2) | protein | 377 | 13% helix, 39% strand | O34714 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A
- CO3 · Carbonate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.37 | 0.75 | 21 | empty |
| 2 | 65 | 0.30 | 0.73 | 13 | empty |
| 3 | 64 | 0.29 | 0.73 | 16 | empty |
| 4 | 51 | 0.28 | 0.75 | 15 | empty |
Compared structures
- 3S0M · A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate… · the same entry in another collection · chain A against A, TM-score 1.00
- O34714 · AlphaFold monomer V2.0 prediction for oxalate decarboxylase oxdc (O34714) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O34714
- Elsewhere: RCSB PDB 3S0M · PDBe 3S0M · UniProt O34714
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