Research workbench
Crystal structure of SAM-bound TTHMTA1-PTEP2 complex
Analyse Crystal structure of SAM-bound TTHMTA1-PTEP2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F4T
- Type
- protein
- Length
- 1,370 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mt-A70 family protein; PTEP2
- UniProt
- Q22GC0, A0DWP1
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, H, K | Mt-A70 family protein | protein | 218 | 31% helix, 22% strand | Q22GC0 |
| B, D | PTEP2 | protein | 125 | 51% helix, 5% strand | A0DWP1 |
| G, J | PTEP2 | protein | 124 | 50% helix, 4% strand | A0DWP1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, E, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.77 | 0.81 | 77 | empty |
| 2 | 682 | 0.75 | 0.81 | 72 | empty |
| 3 | 483 | 0.70 | 0.80 | 75 | SAM |
| 4 | 308 | 0.65 | 0.81 | 50 | empty |
| 5 | 209 | 0.65 | 0.83 | 28 | empty |
Interfaces
13 interfaces between chains.
- H–G · 1550 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1541 Ų buried · 11 hydrogen bonds · protein-protein
- E–D · 1508 Ų buried · 11 hydrogen bonds · protein-protein
- K–J · 1472 Ų buried · 15 hydrogen bonds · protein-protein
- H–B · 370 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7F4T · Crystal structure of SAM-bound TthMTA1-Ptep2 complex · the same entry in another collection · chain A against A, 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 Q22GC0
- Every structure of UniProt A0DWP1
- Elsewhere: RCSB PDB 7F4T · PDBe 7F4T · UniProt Q22GC0 · UniProt A0DWP1
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