Research workbench
Inosine 5'-monophosphate dehydrogenase from vibrio cholerae, deletion mutant, complexed with imp
Analyse Inosine 5'-monophosphate dehydrogenase from vibrio cholerae, deletion mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IX2
- Type
- protein
- Length
- 1,332 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
- Q9KTW3
- Ligands
- IMP, K
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 334 | 37% helix, 21% strand | Q9KTW3 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 333 | 35% helix, 22% strand | Q9KTW3 |
| C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 332 | 35% helix, 20% strand | Q9KTW3 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 333 | 35% helix, 20% strand | Q9KTW3 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.75 | 0.84 | 59 | IMP |
| 2 | 312 | 0.74 | 0.87 | 36 | IMP |
| 3 | 550 | 0.74 | 0.82 | 67 | IMP |
| 4 | 324 | 0.74 | 0.86 | 40 | IMP |
| 5 | 664 | 0.65 | 0.75 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2171 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 2150 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 512 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 96 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 91 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4IX2 · Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, complexed… · 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 Q9KTW3
- Elsewhere: RCSB PDB 4IX2 · PDBe 4IX2 · UniProt Q9KTW3
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