Research workbench
Engineered egtd variant egtd-M252V,E282A in complex with tryptophan and sah
Analyse Engineered egtd variant egtd-M252V,E282A in complex with tryptophan and sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PIP
- Type
- protein
- Length
- 1,258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine-specific methyltransferase egtd
- EC
- 2.1.1.44
- UniProt
- A0R5M8
- Ligands
- TRP, SAH, MG, CL
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine-specific methyltransferase egtd (EC 2.1.1.44) | protein | 316 | 44% helix, 24% strand | A0R5M8 |
| B | Histidine-specific methyltransferase egtd (EC 2.1.1.44) | protein | 309 | 43% helix, 26% strand | A0R5M8 |
| C | Histidine-specific methyltransferase egtd (EC 2.1.1.44) | protein | 315 | 43% helix, 25% strand | A0R5M8 |
| D | Histidine-specific methyltransferase egtd (EC 2.1.1.44) | protein | 318 | 42% helix, 26% strand | A0R5M8 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 4 copies · chains A, B, C, D
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, C
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.88 | 0.90 | 135 | TRP, SAH |
| 2 | 618 | 0.82 | 0.87 | 81 | TRP, SAH |
| 3 | 453 | 0.81 | 0.88 | 68 | TRP, SAH |
| 4 | 350 | 0.63 | 0.79 | 47 | empty |
| 5 | 104 | 0.57 | 0.86 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–D · 355 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 282 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 265 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 199 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 159 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4PIP · Engineered EgtD variant EgtD-M252V,E282A in complex with tryptophan and SAH · the same entry in another collection · chain D against D, TM-score 1.00
- A0R5M8 · AlphaFold monomer V2.0 prediction for histidine N-alpha- methyltransferase (A0R5M8) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 A0R5M8
- Elsewhere: RCSB PDB 4PIP · PDBe 4PIP · UniProt A0R5M8
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