Research workbench
Ternary complex of the human type II inosine monophosphate dedhydrogenase with 6CL-imp and NAD
Analyse Ternary complex of the human type II inosine monophosphate dedhydrogenase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NFB
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase 2
- EC
- 1.1.1.205
- UniProt
- P12268
- Ligands
- CPR, NAD
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 396 | 33% helix, 13% strand | P12268 |
Ligands and binding sites
- CPR · 6-chloropurine riboside, 5'-monophosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.69 | 0.80 | 45 | CPR, NAD |
| 2 | 450 | 0.69 | 0.80 | 47 | CPR, NAD |
| 3 | 324 | 0.55 | 0.75 | 48 | empty |
| 4 | 206 | 0.49 | 0.76 | 26 | empty |
| 5 | 238 | 0.48 | 0.74 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 297 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1NFB · Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with 6Cl-IMP… · the same entry in another collection · chain B against B, 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 0.89
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 1NFB · PDBe 1NFB · UniProt P12268
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