MolNFT v1 · #92896 · protein
NADP+ bound structure of a thiazolinyl imine reductase from yersinia enterocolitica (IRP3)
4GMG · Yersiniabactin biosynthetic protein ybtu: “NADP+ bound structure of a thiazolinyl imine reductase from yersinia enterocolitica (IRP3)”. X-ray diffraction, 1 ligand (NAP), 19 pockets (best druggability 0.83). MolNFT v1 #92896 on…
- PDB
- 4GMG
- Type
- protein
- Length
- 1,382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yersiniabactin biosynthetic protein ybtu
- UniProt
- A1JTG0
- Ligands
- NAP
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yersiniabactin biosynthetic protein ybtu | protein | 358 | 36% helix, 23% strand | A1JTG0 |
| B | Yersiniabactin biosynthetic protein ybtu | protein | 345 | 36% helix, 24% strand | A1JTG0 |
| C | Yersiniabactin biosynthetic protein ybtu | protein | 336 | 39% helix, 24% strand | A1JTG0 |
| D | Yersiniabactin biosynthetic protein ybtu | protein | 343 | 36% helix, 24% strand | A1JTG0 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.83 | 0.84 | 91 | NAP |
| 2 | 1031 | 0.82 | 0.83 | 106 | empty |
| 3 | 96 | 0.79 | 0.99 | 19 | empty |
| 4 | 95 | 0.79 | 0.99 | 19 | empty |
| 5 | 774 | 0.78 | 0.82 | 79 | NAP |
Interfaces
5 interfaces between chains.
- A–B · 4134 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 3697 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 503 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 76 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4GMG · NADP+ bound structure of a Thiazolinyl Imine Reductase from Yersinia enterocolitica (Irp3) · 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 A1JTG0
- Elsewhere: RCSB PDB 4GMG · PDBe 4GMG · UniProt A1JTG0
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