Research workbench
Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with pyrimidineamine inhibitor UTSAM568
Analyse Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BM7
- Type
- protein
- Length
- 1,278 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.98
- Source
- Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
- Molecule
- S-adenosylmethionine decarboxylase beta chain; S-adenosylmethionine decarboxylase alpha…
- EC
- 4.1.1.50
- UniProt
- Q587A7, A5HNV6
- Ligands
- DY7, PUT
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.98 · 5 distinct chains · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 77 | 32% helix, 29% strand | Q587A7 |
| B, D | S-adenosylmethionine decarboxylase alpha chain (EC 4.1.1.50) | protein | 271 | 27% helix, 37% strand | Q587A7 |
| C | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 79 | 27% helix, 27% strand | Q587A7 |
| E | Inactive S-adenosylmethionine decarboxylase prozyme | protein | 291 | 21% helix, 40% strand | A5HNV6 |
| F | Inactive S-adenosylmethionine decarboxylase prozyme | protein | 289 | 22% helix, 42% strand | A5HNV6 |
Ligands and binding sites
- DY7 · 2-amino-4-[(3,5-dibromophenyl)amino]-6-methylpyrimidin-1-ium · ligand · 2 copies · chains A, B, C, D
- PUT · 1,4-diaminobutane · ligand · 2 copies · chains E, F
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains E
- PG4 · Tetraethylene glycol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.73 | 0.99 | 19 | empty |
| 2 | 247 | 0.64 | 0.82 | 41 | B3P |
| 3 | 143 | 0.62 | 0.85 | 27 | DY7 |
| 4 | 252 | 0.61 | 0.80 | 41 | B3P |
| 5 | 119 | 0.60 | 0.85 | 26 | DY7 |
Interfaces
12 interfaces between chains.
- C–D · 3640 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3630 Ų buried · 61 hydrogen bonds · protein-protein
- B–F · 1120 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1113 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 714 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6BM7 · Crystal structure of trypanosoma brucei ADOMETDC/PROZYME heterodimer in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- A5HNV6 · AlphaFold monomer V2.0 prediction for inactive S-adenosylmethionine decarboxylase prozyme… · a predicted model of the same protein · chain E against A, TM-score 0.96
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 Q587A7
- Every structure of UniProt A5HNV6
- Elsewhere: RCSB PDB 6BM7 · PDBe 6BM7 · UniProt Q587A7 · UniProt A5HNV6
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