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Inosine 5'-monophosphate dehydrogenase from vibrio cholerae, deletion mutant, in complex with xmp and NAD
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
- 4X3Z
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- 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
- XMP, NAD, K, PO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 342 | 37% helix, 18% strand | Q9KTW3 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 348 | 35% helix, 19% strand | Q9KTW3 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.77 | 0.85 | 58 | XMP, NAD |
| 2 | 352 | 0.74 | 0.85 | 39 | XMP, NAD |
| 3 | 370 | 0.57 | 0.75 | 43 | empty |
| 4 | 261 | 0.52 | 0.75 | 24 | empty |
| 5 | 215 | 0.50 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4X3Z · Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex… · 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 4X3Z · PDBe 4X3Z · UniProt Q9KTW3
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