Research workbench
Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from bacillus anthracis in the complex with inhibitor oxanosine monophosphate
Analyse Crystal structure of the catalytic domain of the inosine monophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MGU
- Type
- protein
- Length
- 695 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
- A0A0J1HJU0
- Ligands
- JQS, K
- Pockets
- 7 · best druggability 0.77
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 | 348 | 38% helix, 20% strand | A0A0J1HJU0 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 347 | 38% helix, 20% strand | A0A0J1HJU0 |
Ligands and binding sites
- JQS · 5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.77 | 0.86 | 40 | JQS |
| 2 | 375 | 0.74 | 0.85 | 39 | JQS |
| 3 | 834 | 0.70 | 0.76 | 93 | EDO, PEG |
| 4 | 278 | 0.54 | 0.75 | 25 | empty |
| 5 | 227 | 0.53 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 373 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6MGU · Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from… · 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 A0A0J1HJU0
- Elsewhere: RCSB PDB 6MGU · PDBe 6MGU · UniProt A0A0J1HJU0
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