Research workbench
Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from cryptosporidium parvum
Analyse Crystal structure of the catalytic domain of the inosine monophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IXH
- Type
- protein
- Length
- 1,340 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
- Q8T6T2
- Ligands
- IMP, Q21
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 336 | 38% helix, 23% strand | Q8T6T2 |
| B, D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 334 | 37% helix, 23% strand | Q8T6T2 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- Q21 · (2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide · ligand · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.81 | 0.85 | 61 | Q21, IMP |
| 2 | 934 | 0.80 | 0.82 | 82 | EDO, IMP, Q21 |
| 3 | 717 | 0.79 | 0.84 | 59 | IMP, Q21 |
| 4 | 697 | 0.79 | 0.84 | 62 | IMP, Q21 |
| 5 | 293 | 0.68 | 0.83 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2247 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2217 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 2204 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2178 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4IXH · 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
- Q8T6T2 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase (Q8T6T2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8T6T2
- Elsewhere: RCSB PDB 4IXH · PDBe 4IXH · UniProt Q8T6T2
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