Research workbench
Crystal structure of the inosine 5'-monophosphate dehydrogenase with an internal deletion of the cbs domain from bacillus anthracis str. ames complexed with inhibitor Q21
Analyse Crystal structure of the inosine 5'-monophosphate dehydrogenase with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MY8
- Type
- protein
- Length
- 1,334 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
- Q81W29
- Ligands
- IMP, Q21
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 335 | 39% helix, 20% strand | Q81W29 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 331 | 38% helix, 20% strand | Q81W29 |
| C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 332 | 40% helix, 22% strand | Q81W29 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 336 | 39% helix, 21% strand | Q81W29 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- Q21 · (2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide · ligand · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 2 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.80 | 0.82 | 88 | EDO, IMP, Q21 |
| 2 | 768 | 0.79 | 0.83 | 70 | Q21, IMP |
| 3 | 497 | 0.76 | 0.84 | 49 | IMP, Q21 |
| 4 | 459 | 0.75 | 0.84 | 45 | IMP, Q21 |
| 5 | 656 | 0.67 | 0.76 | 63 | EDO |
Interfaces
4 interfaces between chains.
- A–D · 1956 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1904 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 438 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 75 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4MY8 · Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion… · 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 4MY8 · PDBe 4MY8 · UniProt Q81W29
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