MolNFT v1 · #118285 · protein
Crystal structure of oxalate oxidoreductase from moorella thermoacetica bound with carboxy-di-oxido-methyl-tpp (coom-tpp) intermediate
5EXD · Oxalate oxidoreductase subunit alpha: “Crystal structure of oxalate oxidoreductase from moorella thermoacetica bound with…”. X-ray diffraction, 4 ligands (SF4, TPP, O2T), 20 pockets (best druggability 0.81). MolNFT v1 #118285 on…
- PDB
- 5EXD
- Type
- protein
- Length
- 3,969 residues
- Chains
- 12
- 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, O2T, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | 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 | 286 | 29% helix, 23% strand | Q2RI40 |
| C | Oxalate oxidoreductase subunit beta (EC 1.2.7.10) | protein | 312 | 35% helix, 16% strand | Q2RI42 |
| E | Oxalate oxidoreductase subunit delta (EC 1.2.7.10) | protein | 295 | 27% helix, 22% strand | Q2RI40 |
| F, L | Oxalate oxidoreductase subunit beta (EC 1.2.7.10) | protein | 310 | 35% helix, 16% strand | Q2RI42 |
| H | Oxalate oxidoreductase subunit delta (EC 1.2.7.10) | protein | 291 | 30% helix, 22% strand | Q2RI40 |
| I | Oxalate oxidoreductase subunit beta (EC 1.2.7.10) | protein | 309 | 36% helix, 15% strand | Q2RI42 |
| K | Oxalate oxidoreductase subunit delta (EC 1.2.7.10) | protein | 280 | 29% helix, 23% strand | Q2RI40 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains B, C, E, F, H, I, K, L
- TPP · Thiamine diphosphate · ligand · 3 copies · chains A, C, D, G, I, J, L
- O2T · [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[1,1,2-tris(oxidanyl)-2-oxidanylidene-ethyl]-1,3-thiazol-3-ium-5-yl]ethoxy-oxidanyl-phosphoryl] hydrogen phosphate · ligand · chains A, D, F
- MG · Magnesium ion · metal · 4 copies · chains C, F, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.81 | 0.98 | 30 | O2T, MG |
| 2 | 139 | 0.81 | 0.98 | 32 | TPP |
| 3 | 132 | 0.80 | 0.97 | 31 | TPP |
| 4 | 130 | 0.78 | 0.96 | 32 | TPP, MG |
| 5 | 94 | 0.78 | 0.98 | 26 | empty |
Interfaces
29 interfaces between chains.
- A–D · 3297 Ų buried · 44 hydrogen bonds · protein-protein
- G–J · 3278 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 2033 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 1819 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1811 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5EXD · Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with… · the same entry in another collection · chain L against L, 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 Q2RI41
- Every structure of UniProt Q2RI40
- Every structure of UniProt Q2RI42
- Elsewhere: RCSB PDB 5EXD · PDBe 5EXD · UniProt Q2RI41 · UniProt Q2RI40 · UniProt Q2RI42
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