Research workbench
Crystal structure of inosine 5'-monophosphate dehydrogenase from clostridium perfringens complexed with imp and A110
Analyse Crystal structure of inosine 5'-monophosphate dehydrogenase from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q33
- Type
- protein
- Length
- 2,746 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- Q0TN42
- Ligands
- IMP, 2YA, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 344 | 35% helix, 24% strand | Q0TN42 |
| B, D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 342 | 35% helix, 22% strand | Q0TN42 |
| C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 343 | 34% helix, 22% strand | Q0TN42 |
| E | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 343 | 36% helix, 22% strand | Q0TN42 |
| F | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 344 | 35% helix, 23% strand | Q0TN42 |
| G, H | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 344 | 35% helix, 23% strand | Q0TN42 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 2YA · 4-[(1R)-1-[1-(4-chlorophenyl)-1,2,3-triazol-4-yl]ethoxy]-1-oxidanyl-quinoline · ligand · 8 copies · chains A, C, B, D, E, G, F, H
- SO4 · Sulfate ion · ion · chains E
- FMT · Formic acid · additive · 7 copies · chains E, F, G, H
- GOL · Glycerol · additive · 2 copies · chains F
- ACY · Acetic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.82 | 0.84 | 77 | IMP, 2YA |
| 2 | 995 | 0.81 | 0.83 | 93 | IMP, 2YA, FMT |
| 3 | 990 | 0.81 | 0.82 | 84 | IMP, 2YA |
| 4 | 941 | 0.81 | 0.82 | 84 | IMP, 2YA |
| 5 | 963 | 0.80 | 0.82 | 84 | 2YA, IMP, ACY |
Interfaces
12 interfaces between chains.
- C–D · 2431 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2420 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2417 Ų buried · 39 hydrogen bonds · protein-protein
- E–G · 2416 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2389 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4Q33 · Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens… · 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 Q0TN42
- Elsewhere: RCSB PDB 4Q33 · PDBe 4Q33 · UniProt Q0TN42
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