MolNFT v1 · #100486 · protein
Crystal structure of the inosine 5'-monophosphate dehydrogenase, with a internal deletion of cbs domain from campylobacter jejuni complexed with inhibitor compound P12
4MZ1 · Inosine-5'-monophosphate dehydrogenase: “Crystal structure of the inosine 5'-monophosphate dehydrogenase, with a internal deletion of cbs domain from…”. X-ray diffraction, 5 ligands (IMP, 2F1, K), 12 pockets (best druggability…
- PDB
- 4MZ1
- Type
- protein
- Length
- 1,069 residues
- Chains
- 3
- 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, 2F1, K, PO4, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 354 | 36% helix, 19% strand | Q0P9J4 |
| C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 361 | 35% helix, 19% strand | Q0P9J4 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 3 copies · chains A, B, C
- 2F1 · 1-(4-bromophenyl)-3-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- ACY · Acetic acid · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.81 | 0.83 | 121 | empty |
| 2 | 1002 | 0.81 | 0.82 | 96 | IMP, 2F1 |
| 3 | 403 | 0.76 | 0.86 | 38 | IMP |
| 4 | 427 | 0.74 | 0.84 | 38 | IMP, 2F1 |
| 5 | 300 | 0.58 | 0.77 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–C · 776 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4MZ1 · Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion… · 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 4MZ1 · PDBe 4MZ1 · UniProt Q0P9J4
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