MolNFT v1 · #118286 · protein
Crystal structure of oxalate oxidoreductase from moorella thermoacetica bound with carboxy-tpp adduct
5EXE · Oxalate oxidoreductase subunit alpha: “Crystal structure of oxalate oxidoreductase from moorella thermoacetica bound with carboxy-tpp adduct”. X-ray diffraction, 4 ligands (SF4, 5SR, MG), 20 pockets (best druggability 0.81). MolNFT…
- PDB
- 5EXE
- Type
- protein
- Length
- 2,014 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxalate oxidoreductase subunit alpha; Oxalate oxidoreductase subunit delta; Oxalate…
- EC
- 1.2.7.10
- UniProt
- Q2RI41, Q2RI40, Q2RI42
- Ligands
- SF4, 5SR, MG, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Oxalate oxidoreductase subunit alpha (EC 1.2.7.10) | protein | 394 | 42% helix, 18% strand | Q2RI41 |
| B | Oxalate oxidoreductase subunit delta (EC 1.2.7.10) | protein | 309 | 28% helix, 21% strand | Q2RI40 |
| C | Oxalate oxidoreductase subunit beta (EC 1.2.7.10) | protein | 314 | 36% helix, 16% strand | Q2RI42 |
| E | Oxalate oxidoreductase subunit delta (EC 1.2.7.10) | protein | 290 | 29% helix, 22% strand | Q2RI40 |
| F | Oxalate oxidoreductase subunit beta (EC 1.2.7.10) | protein | 313 | 35% helix, 16% strand | Q2RI42 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, C, E, F
- 5SR · [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-carboxy-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-oxidanyl-phosphoryl] hydrogen phosphate · ligand · 2 copies · chains A, C, D, F
- MG · Magnesium ion · metal · 3 copies · chains C, F
- NA · Sodium ion · metal · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.81 | 0.98 | 36 | 5SR, MG |
| 2 | 151 | 0.80 | 0.97 | 35 | 5SR |
| 3 | 79 | 0.77 | 0.99 | 27 | empty |
| 4 | 74 | 0.76 | 0.99 | 24 | empty |
| 5 | 779 | 0.70 | 0.76 | 76 | empty |
Interfaces
12 interfaces between chains.
- A–D · 3357 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 2048 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1845 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1716 Ų buried · 31 hydrogen bonds · protein-protein
- A–F · 1665 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5EXE · Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q2RI41 · AlphaFold monomer V2.0 prediction for oxalate oxidoreductase subunit alpha (Q2RI41) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q2RI42 · AlphaFold monomer V2.0 prediction for oxalate oxidoreductase subunit beta (Q2RI42) · a predicted model of the same protein · chain F against A, TM-score 0.99
- Q2RI40 · AlphaFold monomer V2.0 prediction for oxalate oxidoreductase subunit delta (Q2RI40) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 Q2RI41
- Every structure of UniProt Q2RI40
- Every structure of UniProt Q2RI42
- Elsewhere: RCSB PDB 5EXE · PDBe 5EXE · UniProt Q2RI41 · UniProt Q2RI40 · UniProt Q2RI42
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