MolNFT v1 · #88724 · protein
Imine reductase from nocardiopsis halophila
4D3S: “Imine reductase from nocardiopsis halophila”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #88724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4D3S
- Type
- protein
- Length
- 2,232 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imine reductase
- EC
- 1.5.1.3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Imine reductase (EC 1.5.1.3) | protein | 285 | 55% helix, 13% strand | — |
| B | Imine reductase (EC 1.5.1.3) | protein | 282 | 55% helix, 13% strand | — |
| C, F | Imine reductase (EC 1.5.1.3) | protein | 283 | 56% helix, 14% strand | — |
| D | Imine reductase (EC 1.5.1.3) | protein | 285 | 56% helix, 13% strand | — |
| E | Imine reductase (EC 1.5.1.3) | protein | 267 | 56% helix, 12% strand | — |
| G | Imine reductase (EC 1.5.1.3) | protein | 269 | 55% helix, 9% strand | — |
| H | Imine reductase (EC 1.5.1.3) | protein | 278 | 55% helix, 13% strand | — |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains C, F, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.81 | 0.88 | 52 | BOG |
| 2 | 1189 | 0.81 | 0.82 | 102 | empty |
| 3 | 958 | 0.81 | 0.82 | 86 | empty |
| 4 | 805 | 0.79 | 0.82 | 77 | empty |
| 5 | 632 | 0.78 | 0.83 | 64 | BOG |
Interfaces
16 interfaces between chains.
- C–F · 4362 Ų buried · 29 hydrogen bonds · protein-protein
- B–G · 4222 Ų buried · 26 hydrogen bonds · protein-protein
- A–H · 4204 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 4160 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 513 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4D3S · Imine reductase from Nocardiopsis halophila · 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
- Elsewhere: RCSB PDB 4D3S · PDBe 4D3S
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