Research workbench
Crystal structure of trypanosoma brucei ADOMETDC/PROZYME heterodimer
Analyse Crystal structure of trypanosoma brucei ADOMETDC/PROZYME heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TVM
- Type
- protein
- Length
- 1,290 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, Q587B3
- Ligands
- PYR, PUT
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 78 | 32% helix, 28% strand | Q587A7 |
| B | 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 | 80 | 34% helix, 28% strand | Q587A7 |
| D | S-adenosylmethionine decarboxylase alpha chain (EC 4.1.1.50) | protein | 270 | 27% helix, 37% strand | Q587A7 |
| E | S-adenosylmethionine decarboxylase proenzyme-like, putative (EC 4.1.1.50) | protein | 296 | 21% helix, 38% strand | Q587B3 |
| F | S-adenosylmethionine decarboxylase proenzyme-like, putative (EC 4.1.1.50) | protein | 295 | 21% helix, 39% strand | Q587B3 |
Ligands and binding sites
- PYR · Pyruvic acid · 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.67 | 0.87 | 29 | PYR |
| 2 | 179 | 0.65 | 0.85 | 29 | PYR |
| 3 | 322 | 0.65 | 0.80 | 42 | B3P |
| 4 | 306 | 0.64 | 0.80 | 49 | B3P |
| 5 | 337 | 0.63 | 0.79 | 60 | empty |
Interfaces
12 interfaces between chains.
- A–B · 3642 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3602 Ų buried · 54 hydrogen bonds · protein-protein
- B–F · 1127 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1085 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 690 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5TVM · Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer · 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 Q587A7
- Every structure of UniProt Q587B3
- Elsewhere: RCSB PDB 5TVM · PDBe 5TVM · UniProt Q587A7 · UniProt Q587B3
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