MolNFT v1 · #136402 · protein
Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from bacillus anthracis in the complex with imp and the inhibitor P178
5URS · Inosine-5'-monophosphate dehydrogenase: “Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from bacillus anthracis…”. X-ray diffraction, 4 ligands (IMP, 8LA, K), 20 pockets (best druggability…
- 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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