Research workbench
Structure of an oxalate oxidoreductase
Analyse Structure of an oxalate oxidoreductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C4I
- Type
- protein
- Length
- 2,031 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, TPP, NA, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxalate oxidoreductase subunit alpha (EC 1.2.7.10) | protein | 394 | 41% helix, 18% strand | Q2RI41 |
| B | Oxalate oxidoreductase subunit delta (EC 1.2.7.10) | protein | 308 | 29% helix, 21% strand | Q2RI40 |
| C, F | Oxalate oxidoreductase subunit beta (EC 1.2.7.10) | protein | 312 | 34% helix, 15% strand | Q2RI42 |
| D | Oxalate oxidoreductase subunit alpha (EC 1.2.7.10) | protein | 393 | 41% helix, 18% strand | Q2RI41 |
| E | Oxalate oxidoreductase subunit delta (EC 1.2.7.10) | protein | 312 | 26% helix, 21% strand | Q2RI40 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, C, E, F
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, C, D, F
- NA · Sodium ion · metal · 2 copies · chains B, F
- MG · Magnesium ion · metal · 2 copies · chains C, 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 | 152 | 0.81 | 0.97 | 33 | TPP, MG |
| 2 | 144 | 0.81 | 0.98 | 35 | TPP |
| 3 | 84 | 0.78 | 0.99 | 26 | empty |
| 4 | 85 | 0.77 | 0.99 | 24 | empty |
| 5 | 75 | 0.74 | 0.98 | 21 | empty |
Interfaces
12 interfaces between chains.
- A–D · 3436 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 2117 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2033 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 1725 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1700 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5C4I · Structure of an Oxalate Oxidoreductase · 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 D 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 C 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 B against A, TM-score 0.95
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 5C4I · PDBe 5C4I · UniProt Q2RI41 · UniProt Q2RI40 · UniProt Q2RI42
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.