MolNFT v1 · #118412 · protein
Structure of mn bound DUF89 from saccharomyces cerevisiae
5F13 · Protein-glutamate O-methyltransferase: “Structure of mn bound DUF89 from saccharomyces cerevisiae”. X-ray diffraction, 3 ligands (MN, PO4, CL), 14 pockets (best druggability 0.74). MolNFT v1 #118412 on GenesisL1: 3D structure…
- PDB
- 5F13
- Type
- protein
- Length
- 1,338 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-glutamate O-methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q04371
- Ligands
- MN, PO4, CL
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-glutamate O-methyltransferase (EC 2.1.1.-) | protein | 445 | 55% helix, 11% strand | Q04371 |
| B | Protein-glutamate O-methyltransferase (EC 2.1.1.-) | protein | 449 | 55% helix, 11% strand | Q04371 |
| C | Protein-glutamate O-methyltransferase (EC 2.1.1.-) | protein | 444 | 57% helix, 11% strand | Q04371 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.74 | 0.78 | 87 | EDO |
| 2 | 369 | 0.64 | 0.79 | 42 | MN, PO4 |
| 3 | 339 | 0.60 | 0.77 | 40 | MN, PO4 |
| 4 | 323 | 0.58 | 0.77 | 35 | MN, PO4 |
| 5 | 351 | 0.56 | 0.74 | 38 | empty |
Interfaces
2 interfaces between chains.
- B–C · 616 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 369 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5F13 · Structure of Mn bound DUF89 from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- Q04371 · AlphaFold monomer V2.0 prediction for damage-control phosphatase YMR027W (Q04371) · a predicted model of the same protein · chain C 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 Q04371
- Elsewhere: RCSB PDB 5F13 · PDBe 5F13 · UniProt Q04371
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