MolNFT v1 · #75181 · protein
Crystal structure of MXR1 from saccharomyces cerevisiae in unusual oxidized form
3PIM · Peptide methionine sulfoxide reductase: “Crystal structure of MXR1 from saccharomyces cerevisiae in unusual oxidized form”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1 #75181 on GenesisL1: 3D structure, binding…
- PDB
- 3PIM
- Type
- protein
- Length
- 513 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide methionine sulfoxide reductase
- EC
- 1.8.4.11
- UniProt
- P40029
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide methionine sulfoxide reductase (EC 1.8.4.11) | protein | 173 | 32% helix, 24% strand | P40029 |
| B | Peptide methionine sulfoxide reductase (EC 1.8.4.11) | protein | 177 | 32% helix, 24% strand | P40029 |
| C | Peptide methionine sulfoxide reductase (EC 1.8.4.11) | protein | 163 | 29% helix, 25% strand | P40029 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.70 | 0.81 | 62 | empty |
| 2 | 151 | 0.52 | 0.79 | 34 | empty |
| 3 | 269 | 0.51 | 0.74 | 29 | empty |
| 4 | 102 | 0.48 | 0.81 | 20 | empty |
| 5 | 149 | 0.45 | 0.76 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1547 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 328 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3PIM · Crystal structure of Mxr1 from Saccharomyces cerevisiae in unusual oxidized form · the same entry in another collection · chain A against A, TM-score 1.00
- P40029 · AlphaFold monomer V2.0 prediction for peptide methionine sulfoxide reductase (P40029) · a predicted model of the same protein · chain C against A, TM-score 0.81
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 P40029
- Elsewhere: RCSB PDB 3PIM · PDBe 3PIM · UniProt P40029
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