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The crystal structure of the complex between imp dehydrogenase catalytic domain and a transition state analogue mzp
Analyse The crystal structure of the complex between imp dehydrogenase catalytic domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PVN
- Type
- protein
- Length
- 1,448 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
- P50097
- Ligands
- MZP, K
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 362 | 38% helix, 22% strand | P50097 |
Ligands and binding sites
- MZP · 4-carbamoyl-1-beta-D-ribofuranosyl-imidazolium-5-olate-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 8 copies · chains A, D, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.80 | 0.98 | 37 | MZP |
| 2 | 133 | 0.80 | 0.98 | 35 | MZP |
| 3 | 140 | 0.80 | 0.97 | 34 | MZP |
| 4 | 133 | 0.79 | 0.97 | 35 | MZP |
| 5 | 798 | 0.68 | 0.75 | 64 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2191 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2164 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2158 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 2130 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1PVN · The crystal structure of the complex between IMP dehydrogenase catalytic domain and a… · the same entry in another collection · chain C against C, TM-score 1.00
- P50097 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase (P50097) · a predicted model of the same protein · chain A 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 P50097
- Elsewhere: RCSB PDB 1PVN · PDBe 1PVN · UniProt P50097
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