Research workbench
Crystal structure of SAM-bound MTA1-P1-P2 complex
Analyse Crystal structure of SAM-bound MTA1-P1-P2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F4M
- Type
- protein
- Length
- 752 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein, putative; Mt-A70 family protein; P1 protein
- UniProt
- I7M8B9, Q22GC0, Q22VV9
- Ligands
- SAM
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transmembrane protein, putative | protein | 130 | 52% helix, 5% strand | I7M8B9 |
| C | Mt-A70 family protein | protein | 215 | 33% helix, 20% strand | Q22GC0 |
| D | Mt-A70 family protein | protein | 216 | 31% helix, 19% strand | Q22GC0 |
| E | P1 protein | protein | 37 | 65% helix, 0% strand | Q22VV9 |
| F | P1 protein | protein | 25 | 80% helix, 0% strand | Q22VV9 |
| A | Transmembrane protein, putative | protein | 129 | 53% helix, 5% strand | I7M8B9 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.53 | 0.80 | 28 | SAM |
| 2 | 193 | 0.51 | 0.77 | 32 | empty |
| 3 | 186 | 0.49 | 0.76 | 29 | empty |
| 4 | 139 | 0.45 | 0.77 | 25 | SAM |
| 5 | 94 | 0.43 | 0.78 | 17 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1754 Ų buried · 17 hydrogen bonds · protein-protein
- D–A · 1739 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1114 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 860 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 781 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7F4M · Crystal structure of SAM-bound MTA1-p1-p2 complex · the same entry in another collection · chain B against B, 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 I7M8B9
- Every structure of UniProt Q22GC0
- Every structure of UniProt Q22VV9
- Elsewhere: RCSB PDB 7F4M · PDBe 7F4M · UniProt I7M8B9 · UniProt Q22GC0 · UniProt Q22VV9
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