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 C91
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
- 4MY9
- Type
- protein
- Length
- 2,792 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, C91
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 350 | 37% helix, 22% strand | Q81W29 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 351 | 36% helix, 22% strand | Q81W29 |
| C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 347 | 38% helix, 22% strand | Q81W29 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 347 | 37% helix, 22% strand | Q81W29 |
| E | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 349 | 38% helix, 22% strand | Q81W29 |
| F, H | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 348 | 38% helix, 23% strand | Q81W29 |
| G | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 352 | 38% helix, 23% strand | Q81W29 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- C91 · N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide · ligand · 8 copies · chains A, C, B, D, E, F, H, G
- MLI · Malonate ion · additive · 9 copies · chains A, B, D, C, E, G, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.81 | 0.82 | 85 | IMP, C91 |
| 2 | 708 | 0.80 | 0.84 | 66 | IMP, C91 |
| 3 | 706 | 0.80 | 0.84 | 61 | IMP, C91 |
| 4 | 660 | 0.79 | 0.84 | 58 | IMP, C91 |
| 5 | 629 | 0.79 | 0.84 | 62 | IMP, C91 |
Interfaces
14 interfaces between chains.
- E–G · 2654 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 2623 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2603 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2601 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2600 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 4MY9 · 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 4MY9 · PDBe 4MY9 · UniProt Q81W29
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