MolNFT v1 · #156836 · protein
Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from campylobacter jejuni in the complex with inhibitor oxanosine monophosphate
6MGR: “Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from campylobacter…”. X-ray diffraction, 4 ligands (JQS, K, SO4), 17 pockets (best druggability 0.87). MolNFT v1 #156836 on GenesisL1: 3D…
- 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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