MolNFT v1 · #136358 · protein
Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from campylobacter jejuni in the complex with inhibitor P182
5UQH · Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'…: “Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from campylobacter…”. X-ray diffraction, 3 ligands (IMP, 8L1, K), 20 pockets (best…
- PDB
- 5UQH
- Type
- protein
- Length
- 2,865 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- A0A1B3XFT6, A5KFK9
- Ligands
- IMP, 8L1, K
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 368 | 38% helix, 21% strand | A0A1B3XFT6, A5KFK9 |
| B | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 358 | 35% helix, 22% strand | A0A1B3XFT6, A5KFK9 |
| C | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 356 | 37% helix, 21% strand | A0A1B3XFT6, A5KFK9 |
| D | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 355 | 35% helix, 22% strand | A0A1B3XFT6, A5KFK9 |
| E | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 357 | 36% helix, 22% strand | A0A1B3XFT6, A5KFK9 |
| F | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 361 | 36% helix, 22% strand | A0A1B3XFT6, A5KFK9 |
| G | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 354 | 35% helix, 21% strand | A0A1B3XFT6, A5KFK9 |
| H | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 356 | 36% helix, 22% strand | A0A1B3XFT6, A5KFK9 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 8L1 · N-{4-chloro-3-[4-(trifluoromethyl)-1,3-thiazol-2-yl]phenyl}-N'-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, H, F, G
- EDO · 1,2-ethanediol · additive · 5 copies · chains D, E, F
- IPA · Isopropyl alcohol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.81 | 0.82 | 96 | empty |
| 2 | 896 | 0.80 | 0.82 | 86 | IMP, 8L1 |
| 3 | 891 | 0.80 | 0.82 | 82 | IMP, 8L1 |
| 4 | 816 | 0.79 | 0.82 | 77 | IMP, 8L1, EDO |
| 5 | 526 | 0.78 | 0.85 | 60 | IMP, 8L1 |
Interfaces
15 interfaces between chains.
- A–B · 2439 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2424 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2408 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2395 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2395 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5UQH · 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 A0A1B3XFT6
- Every structure of UniProt A5KFK9
- Elsewhere: RCSB PDB 5UQH · PDBe 5UQH · UniProt A0A1B3XFT6 · UniProt A5KFK9
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