Research workbench
Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from campylobacter jejuni 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
- 6MGR
- Type
- protein
- Length
- 1,449 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- A0A2R4D3F6
- Ligands
- JQS, K, SO4, CL
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine monophosphate dehydrogenase (EC 1.1.1.205) | protein | 361 | 36% helix, 22% strand | A0A2R4D3F6 |
| B | Inosine monophosphate dehydrogenase (EC 1.1.1.205) | protein | 359 | 36% helix, 21% strand | A0A2R4D3F6 |
| C | Inosine monophosphate dehydrogenase (EC 1.1.1.205) | protein | 369 | 36% helix, 21% strand | A0A2R4D3F6 |
| D | Inosine monophosphate dehydrogenase (EC 1.1.1.205) | protein | 360 | 37% helix, 22% strand | A0A2R4D3F6 |
Ligands and binding sites
- JQS · 5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 5 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.87 | 0.95 | 52 | JQS, SO4, MPD |
| 2 | 460 | 0.82 | 0.89 | 50 | JQS, SO4 |
| 3 | 443 | 0.81 | 0.89 | 46 | JQS, SO4, MPD |
| 4 | 450 | 0.81 | 0.89 | 48 | JQS, SO4, MPD |
| 5 | 623 | 0.75 | 0.81 | 58 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2615 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2496 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2480 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2467 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6MGR · 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 A0A2R4D3F6
- Elsewhere: RCSB PDB 6MGR · PDBe 6MGR · UniProt A0A2R4D3F6
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