MolNFT v1 · #13909 · protein
Crystal structure of ternary complex of tritrichomonas foetus inosine- 5'-monophosphate dehydrogenase: structural characterization of NAD+ site in microbial enzyme
1LRT · Inosine-5'-monophosphate dehydrogenase: “Crystal structure of ternary complex of tritrichomonas foetus inosine- 5'-monophosphate dehydrogenase…”. X-ray diffraction, 3 ligands (IMP, TAD, K), 8 pockets (best druggability 0.79). MolNFT…
- PDB
- 1LRT
- Type
- protein
- Length
- 1,346 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
- P50097
- Ligands
- IMP, TAD, K
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 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 | 338 | 37% helix, 22% strand | P50097 |
| B, C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 334 | 38% helix, 22% strand | P50097 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 340 | 37% helix, 22% strand | P50097 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- TAD · Beta-methylene-thiazole-4-carboxyamide-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, D, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 12 copies · chains A, B, D, C
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.79 | 0.81 | 82 | IMP, TAD, TRS |
| 2 | 1108 | 0.79 | 0.81 | 105 | IMP, TAD |
| 3 | 1164 | 0.77 | 0.79 | 82 | IMP, TAD |
| 4 | 1159 | 0.76 | 0.79 | 81 | IMP, TAD |
| 5 | 849 | 0.75 | 0.79 | 62 | TRS |
Interfaces
4 interfaces between chains.
- A–D · 1434 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1398 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1396 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1385 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1LRT · Crystal structure of ternary complex of tritrichomonas foetus inosine-5'-monophosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- P50097 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase (P50097) · a predicted model of the same protein · chain B 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 P50097
- Elsewhere: RCSB PDB 1LRT · PDBe 1LRT · UniProt P50097
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