Research workbench
Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from bacillus anthracis in the complex with imp and the inhibitor P178
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
- 5URS
- Type
- protein
- Length
- 2,798 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
- Q81W29
- Ligands
- IMP, 8LA, K, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 351 | 38% helix, 22% strand | Q81W29 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 350 | 37% helix, 22% strand | Q81W29 |
| C, G | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 349 | 37% helix, 22% strand | Q81W29 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 350 | 38% helix, 22% strand | Q81W29 |
| E | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 350 | 38% helix, 22% strand | Q81W29 |
| F | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 351 | 38% helix, 21% strand | Q81W29 |
| H | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 348 | 38% helix, 22% strand | Q81W29 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 8LA · N-[4-chloro-3-(alpha-D-ribofuranosyloxy)phenyl]-N'-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea · ligand · 8 copies · chains A, C, B, D, E, G, F, H
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, D, E, F
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.78 | 0.81 | 76 | IMP, 8LA |
| 2 | 738 | 0.77 | 0.82 | 67 | IMP, 8LA |
| 3 | 610 | 0.77 | 0.83 | 61 | IMP, 8LA |
| 4 | 728 | 0.77 | 0.81 | 69 | IMP, 8LA |
| 5 | 720 | 0.76 | 0.81 | 67 | IMP, 8LA |
Interfaces
15 interfaces between chains.
- G–H · 2684 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 2613 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 2590 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2584 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2578 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 5URS · 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
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 Q81W29
- Elsewhere: RCSB PDB 5URS · PDBe 5URS · UniProt Q81W29
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