Research workbench
Crystal structure of the inosine 5'-monophosphate dehydrogenase, with an internal deletion of cbs domain from campylobacter jejuni complexed with inhibitor compound C91
Analyse Crystal structure of the inosine 5'-monophosphate dehydrogenase, with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MZ8
- Type
- protein
- Length
- 1,406 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- Q0P9J4
- Ligands
- IMP, C91, 2F2, SO4, CL
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 353 | 36% helix, 21% strand | Q0P9J4 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 354 | 34% helix, 21% strand | Q0P9J4 |
| C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 349 | 34% helix, 22% strand | Q0P9J4 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 350 | 36% helix, 21% strand | Q0P9J4 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- C91 · N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide · ligand · 4 copies · chains A, B, C, D
- 2F2 · dimethyl ether · ligand · chains A, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.82 | 0.83 | 117 | IMP, C91, ACY |
| 2 | 619 | 0.78 | 0.83 | 56 | IMP, C91 |
| 3 | 764 | 0.76 | 0.81 | 74 | IMP, C91 |
| 4 | 1043 | 0.76 | 0.78 | 101 | empty |
| 5 | 396 | 0.75 | 0.85 | 37 | IMP, C91 |
Interfaces
5 interfaces between chains.
- A–B · 2319 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2206 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 566 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 563 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 95 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4MZ8 · Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with an Internal… · 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 Q0P9J4
- Elsewhere: RCSB PDB 4MZ8 · PDBe 4MZ8 · UniProt Q0P9J4
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