Research workbench
Structure of the C-terminal domain of the saccharomyces cerevisiae mutl alpha (MLH1/PMS1) heterodimer bound to a fragment of NTG2
Analyse Structure of the C-terminal domain of the saccharomyces cerevisiae mutl alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FMN
- Type
- protein
- Length
- 485 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA mismatch repair protein MLH1; DNA mismatch repair protein PMS1; DNA repair peptide
- UniProt
- P38920, P14242, Q08214
- Ligands
- ACE, ZN
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein MLH1 | protein | 265 | 52% helix, 17% strand | P38920 |
| B | DNA mismatch repair protein PMS1 | protein | 213 | 39% helix, 23% strand | P14242 |
| C | DNA repair peptide | protein | 7 | 0% helix, 0% strand | Q08214 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.52 | 0.79 | 27 | empty |
| 2 | 91 | 0.49 | 0.82 | 15 | empty |
| 3 | 188 | 0.45 | 0.74 | 23 | empty |
| 4 | 77 | 0.33 | 0.74 | 15 | empty |
| 5 | 56 | 0.30 | 0.75 | 12 | GOL, EDO |
Interfaces
2 interfaces between chains.
- A–B · 1866 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 431 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4FMN · Structure of the C-terminal domain of the Saccharomyces cerevisiae MUTL alpha (MLH1/PMS1)… · the same entry in another collection · chain A against A, TM-score 1.00
- P38920 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein MLH1 (P38920) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P14242 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein PMS1 (P14242) · a predicted model of the same protein · chain B against A, TM-score 0.88
- Q08214 · AlphaFold monomer V2.0 prediction for endonuclease III homolog 2 (Q08214) · a predicted model of the same protein · chain C against A, TM-score 0.63
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 P38920
- Every structure of UniProt P14242
- Every structure of UniProt Q08214
- Elsewhere: RCSB PDB 4FMN · PDBe 4FMN · UniProt P38920 · UniProt P14242 · UniProt Q08214
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