Research workbench
NADP+ bound structure of IRP3, a thiazolinyl imine reductase from yersinia enterocolitica
Analyse NADP+ bound structure of IRP3, a thiazolinyl imine reductase from yersinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KVQ
- Type
- protein
- Length
- 709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IRP3 protein
- UniProt
- O54512
- Ligands
- NAP
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IRP3 protein | protein | 354 | 38% helix, 23% strand | O54512 |
| B | IRP3 protein | protein | 355 | 37% helix, 23% strand | O54512 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.81 | 0.83 | 74 | NAP |
| 2 | 865 | 0.80 | 0.83 | 72 | NAP |
| 3 | 99 | 0.80 | 0.99 | 20 | empty |
| 4 | 128 | 0.49 | 0.79 | 38 | empty |
| 5 | 127 | 0.40 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4398 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 5KVQ · NADP+ bound structure of Irp3, a Thiazolinyl Imine Reductase from Yersinia enterocolitica · 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 O54512
- Elsewhere: RCSB PDB 5KVQ · PDBe 5KVQ · UniProt O54512
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