Research workbench
Ternary complex of human type-II inosine monophosphate dehydrogenase with 6-cl-imp and selenazole adenine dinucleotide
Analyse Ternary complex of human type-II inosine monophosphate dehydrogenase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B3O
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (inosine monophosphate dehydrogenase 2)
- EC
- 1.1.1.205
- UniProt
- P12268
- Ligands
- CPR, SAE, UNX
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (inosine monophosphate dehydrogenase 2) (EC 1.1.1.205) | protein | 304 | 39% helix, 17% strand | P12268 |
| B | Protein (inosine monophosphate dehydrogenase 2) (EC 1.1.1.205) | protein | 410 | 30% helix, 16% strand | P12268 |
Ligands and binding sites
- CPR · 6-chloropurine riboside, 5'-monophosphate · ligand · 2 copies · chains A, B
- SAE · Selenazole-4-carboxyamide-adenine dinucleotide · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 15 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.67 | 0.82 | 37 | CPR |
| 2 | 270 | 0.60 | 0.79 | 30 | empty |
| 3 | 280 | 0.51 | 0.74 | 33 | empty |
| 4 | 92 | 0.50 | 0.82 | 21 | empty |
| 5 | 66 | 0.42 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 309 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1B3O · Ternary complex of human type-II inosine monophosphate dehydrogenase with 6-cl-imp and… · the same entry in another collection · chain A against A, TM-score 1.00
- P12268 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase 2 (P12268) · a predicted model of the same protein · chain A 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 P12268
- Elsewhere: RCSB PDB 1B3O · PDBe 1B3O · UniProt P12268
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