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
- 1,276 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine decarboxylase beta chain; S-adenosylmethionine decarboxylase alpha…
- EC
- 4.1.1.50
- UniProt
- Q587A7, A5HNV6
- Ligands
- PYR, DY7, PUT
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 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 | 270 | 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
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B, C, D
- 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 | 150 | 0.68 | 0.88 | 25 | PYR, DY7 |
| 3 | 166 | 0.67 | 0.87 | 28 | PYR, DY7 |
| 4 | 247 | 0.64 | 0.82 | 41 | B3P |
| 5 | 251 | 0.61 | 0.80 | 41 | B3P |
Interfaces
12 interfaces between chains.
- C–D · 3630 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 3617 Ų buried · 60 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 · 715 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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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