MolNFT v1 · #99816 · protein
Assigning the epr fine structure parameters of the MN(II) centers in bacillus subtilis oxalate decarboxylase by site-directed mutagenesis and DFT/MM calculations
4MET · Oxalate decarboxylase oxdc: “Assigning the epr fine structure parameters of the MN(II) centers in bacillus subtilis oxalate decarboxylase…”. X-ray diffraction, 1 ligand (CO), 20 pockets (best druggability 0.65). MolNFT v1 #99816 on…
- PDB
- 4MET
- Type
- protein
- Length
- 1,508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxalate decarboxylase oxdc
- EC
- 4.1.1.2
- UniProt
- O34714
- Ligands
- CO
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Oxalate decarboxylase oxdc (EC 4.1.1.2) | protein | 377 | 15% helix, 39% strand | O34714 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.65 | 0.80 | 39 | empty |
| 2 | 106 | 0.53 | 0.83 | 24 | empty |
| 3 | 183 | 0.48 | 0.76 | 32 | empty |
| 4 | 119 | 0.47 | 0.79 | 22 | empty |
| 5 | 101 | 0.42 | 0.78 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2886 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2885 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 214 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 132 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 82 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4MET · Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis… · 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 4MET · PDBe 4MET · UniProt O34714
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