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Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from mycobacterium tuberculosis
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
- 4ZQR
- Type
- protein
- Length
- 1,429 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- P9WKI7
- Ligands
- K, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 357 | 36% helix, 22% strand | P9WKI7 |
| C | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 358 | 35% helix, 23% strand | P9WKI7 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, D, C, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, B, D
- PGO · S-1,2-propanediol · additive · 15 copies · chains A, D, C, B
- GOL · Glycerol · additive · 11 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.83 | 0.89 | 63 | PO4, PGO |
| 2 | 539 | 0.83 | 0.89 | 62 | PO4, PGO |
| 3 | 551 | 0.83 | 0.89 | 60 | PGO, PO4 |
| 4 | 576 | 0.83 | 0.88 | 62 | PGO, PO4, GOL |
| 5 | 688 | 0.78 | 0.83 | 56 | GOL, PGO |
Interfaces
6 interfaces between chains.
- A–C · 2643 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 2638 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 2633 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 2608 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZQR · 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
- P9WKI7 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase (P9WKI7) · a predicted model of the same protein · chain C 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 P9WKI7
- Elsewhere: RCSB PDB 4ZQR · PDBe 4ZQR · UniProt P9WKI7
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