Research workbench
Crystal structure of trypanosoma brucei ADOMETDC/PROZYME heterodimer in complex with inhibitor cgp 40215
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
- 5TVF
- Type
- protein
- Length
- 1,280 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
- PUT, PYR, CGQ
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 25% 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, 30% strand | Q587A7 |
| B, D | S-adenosylmethionine decarboxylase alpha chain (EC 4.1.1.50) | protein | 270 | 28% helix, 37% strand | Q587A7 |
| C | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 81 | 33% helix, 26% strand | Q587A7 |
| E | S-adenosylmethionine decarboxylase proenzyme-like, putative (EC 4.1.1.50) | protein | 292 | 21% helix, 40% strand | Q587B3 |
| F | S-adenosylmethionine decarboxylase proenzyme-like, putative (EC 4.1.1.50) | protein | 290 | 21% helix, 42% strand | Q587B3 |
Ligands and binding sites
- PUT · 1,4-diaminobutane · ligand · 4 copies · chains A, B, C, D, E, F
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B, C, D
- CGQ · 3-[C-[N'-(3-carbamimidoyl-benzylidenium)-hydrazino]-[[aminomethylidene]aminium]-iminomethyl]-benzamidinium · ligand · 2 copies · chains A, B, C, D
- 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.73 | 0.99 | 20 | empty |
| 2 | 152 | 0.67 | 0.88 | 27 | PYR, CGQ |
| 3 | 194 | 0.64 | 0.84 | 33 | PYR, CGQ |
| 4 | 105 | 0.64 | 0.89 | 29 | PUT |
| 5 | 259 | 0.63 | 0.81 | 41 | B3P |
Interfaces
12 interfaces between chains.
- A–B · 3624 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 3605 Ų buried · 57 hydrogen bonds · protein-protein
- B–F · 1114 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1093 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 705 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5TVF · Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with… · 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 5TVF · PDBe 5TVF · UniProt Q587A7 · UniProt Q587B3
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