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Substrate analog and NADP+ bound structure of IRP3, a thiazolinyl imine reductase from yersinia enterocolitica
Analyse Substrate analog and NADP+ bound structure of IRP3, a thiazolinyl imine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KVS
- Type
- protein
- Length
- 707 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IRP3 protein
- UniProt
- O54512
- Ligands
- NAP, 6XR
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IRP3 protein | protein | 353 | 37% helix, 23% strand | O54512 |
| B | IRP3 protein | protein | 354 | 38% helix, 23% strand | O54512 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 6XR · (4~{R})-2-[2-(2-hydroxyphenyl)-1,3-thiazol-4-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.80 | 0.83 | 67 | NAP, 6XR |
| 2 | 837 | 0.80 | 0.83 | 65 | NAP, 6XR |
| 3 | 110 | 0.80 | 0.99 | 23 | empty |
| 4 | 60 | 0.41 | 0.81 | 15 | empty |
| 5 | 127 | 0.41 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4366 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 5KVS · Substrate Analog and NADP+ bound structure of Irp3, a Thiazolinyl Imine Reductase from… · 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 5KVS · PDBe 5KVS · UniProt O54512
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