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Crystal Structure of the Thermostable NADH4-bound old yellow enzyme from Thermoanaerobacter pseudethanolicus E39
Analyse Crystal Structure of the Thermostable NADH4-bound old yellow enzyme from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KRZ
- Type
- protein
- Length
- 1,338 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Thermoanaerobacter pseudethanolicus ATCC 33223
- Molecule
- NADH:flavin oxidoreductase/NADH oxidase
- UniProt
- B0KAH1
- Ligands
- FMN, TXD
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NADH:flavin oxidoreductase/NADH oxidase | protein | 335 | 39% helix, 16% strand | B0KAH1 |
| B, C | NADH:flavin oxidoreductase/NADH oxidase | protein | 334 | 38% helix, 16% strand | B0KAH1 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- TXD · 1,4,5,6-tetrahydronicotinamide adenine dinucleotide · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.68 | 0.78 | 41 | FMN, TXD |
| 2 | 510 | 0.66 | 0.77 | 50 | FMN, TXD |
| 3 | 482 | 0.65 | 0.77 | 46 | FMN, TXD |
| 4 | 511 | 0.65 | 0.77 | 47 | FMN, TXD |
| 5 | 58 | 0.36 | 0.78 | 11 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1113 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 787 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3KRZ · Crystal structure of the thermostable NADH4-bound old yellow enzyme 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 B0KAH1
- Elsewhere: RCSB PDB 3KRZ · PDBe 3KRZ · UniProt B0KAH1
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