Research workbench
Crystal structure of Enterococcus hirae L-lactate oxidase in complex with D-lactate form ligand
Analyse Crystal structure of Enterococcus hirae L-lactate oxidase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M73
- Type
- protein
- Length
- 364 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Enterococcus hirae ATCC 9790
- Molecule
- L-lactate oxidase
- EC
- 1.1.3.15
- UniProt
- I6SYK8
- Ligands
- FNR, LAC, PYR
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.7 · 1 distinct chain · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate oxidase (EC 1.1.3.15) | protein | 364 | 45% helix, 12% strand | I6SYK8 |
Ligands and binding sites
- FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · chains A
- LAC · Lactic acid · ligand · chains A
- PYR · Pyruvic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PGE · Triethylene glycol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.81 | 0.97 | 33 | FNR, LAC |
| 2 | 148 | 0.50 | 0.79 | 26 | empty |
| 3 | 87 | 0.35 | 0.75 | 19 | TRS |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6M73 · Crystal structure of enterococcus hirae L-lactate oxidase in complex with lactate · 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 I6SYK8
- Elsewhere: RCSB PDB 6M73 · PDBe 6M73 · UniProt I6SYK8
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