MolNFT v1 · #162669 · protein
In cellulo crystallization of trypanosoma brucei imp dehydrogenase enables the identification of ATP and gmp as genuine co-factors
6RFU · Inosine-5'-monophosphate dehydrogenase: “In cellulo crystallization of trypanosoma brucei imp dehydrogenase enables the identification of ATP and gmp…”. X-ray diffraction, 2 ligands (ATP, 5GP), 8 pockets (best druggability 0.71).…
- PDB
- 6RFU
- Type
- protein
- Length
- 893 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- P50098
- Ligands
- ATP, 5GP
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 445 | 38% helix, 20% strand | P50098 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 448 | 37% helix, 20% strand | P50098 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.71 | 0.79 | 47 | ATP |
| 2 | 247 | 0.61 | 0.80 | 28 | 5GP |
| 3 | 229 | 0.60 | 0.80 | 24 | 5GP |
| 4 | 89 | 0.35 | 0.75 | 20 | empty |
| 5 | 52 | 0.35 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1163 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6RFU · In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the… · the same entry in another collection · chain A against A, TM-score 1.00
- P50098 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase (P50098) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 P50098
- Elsewhere: RCSB PDB 6RFU · PDBe 6RFU · UniProt P50098
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