MolNFT v1 · #104816 · protein
Crystal structure of the inosine 5'-monophosphate dehydrogenase with an internal deletion of the cbs domain from bacillus anthracis str. ames complexed with inhibitor D67
4QM1 · Inosine-5'-monophosphate dehydrogenase: “Crystal structure of the inosine 5'-monophosphate dehydrogenase with an internal deletion of the cbs domain…”. X-ray diffraction, 2 ligands (IMP, 39H), 12 pockets (best druggability 0.80).…
- PDB
- 4QM1
- Type
- protein
- Length
- 1,350 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
- Q81W29
- Ligands
- IMP, 39H
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 337 | 39% helix, 21% strand | Q81W29 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 345 | 34% helix, 21% strand | Q81W29 |
| C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 332 | 37% helix, 22% strand | Q81W29 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 336 | 38% helix, 22% strand | Q81W29 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- 39H · 2-(3-methyl-4-oxo-3,4-dihydrophthalazin-1-yl)-N-(6,7,8,9-tetrahydrodibenzo[b,d]furan-2-yl)acetamide · ligand · 4 copies · chains A, B, D, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.80 | 0.81 | 89 | 39H, IMP |
| 2 | 845 | 0.79 | 0.82 | 86 | IMP, 39H |
| 3 | 844 | 0.77 | 0.80 | 83 | 39H, IMP |
| 4 | 824 | 0.77 | 0.80 | 68 | 39H, IMP |
| 5 | 780 | 0.69 | 0.76 | 84 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2188 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 2157 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2142 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1966 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4QM1 · Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an 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 Q81W29
- Elsewhere: RCSB PDB 4QM1 · PDBe 4QM1 · UniProt Q81W29
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