MolNFT v1 · #84324 · protein
R-imine reductase from streptomyces kanamyceticus in complex with NADP.
3ZHB: “R-imine reductase from streptomyces kanamyceticus in complex with NADP.”. X-ray diffraction, 1 ligand (NAP), 6 pockets (best druggability 0.71). MolNFT v1 #84324 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZHB
- Type
- protein
- Length
- 1,153 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R-imine reductase
- EC
- 1.5.1.-
- UniProt
- Q1EQE0
- Ligands
- NAP
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | R-imine reductase (EC 1.5.1.-) | protein | 288 | 54% helix, 14% strand | Q1EQE0 |
| B | R-imine reductase (EC 1.5.1.-) | protein | 285 | 55% helix, 14% strand | Q1EQE0 |
| C | R-imine reductase (EC 1.5.1.-) | protein | 286 | 54% helix, 14% strand | Q1EQE0 |
| D | R-imine reductase (EC 1.5.1.-) | protein | 294 | 54% helix, 14% strand | Q1EQE0 |
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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.71 | 0.77 | 64 | NAP |
| 2 | 674 | 0.70 | 0.77 | 82 | NAP |
| 3 | 699 | 0.70 | 0.77 | 68 | NAP |
| 4 | 628 | 0.69 | 0.77 | 62 | NAP |
| 5 | 293 | 0.60 | 0.78 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3988 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3908 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 298 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 138 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZHB · R-imine reductase from Streptomyces kanamyceticus in complex with NADP. · 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 Q1EQE0
- Elsewhere: RCSB PDB 3ZHB · PDBe 3ZHB · UniProt Q1EQE0
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