MolNFT v1 · #105918 · protein
Aerococcus viridans L-lactate oxidase mutant
4RJE: “Aerococcus viridans L-lactate oxidase mutant”. X-ray diffraction, 2 ligands (FNR, PYR), 12 pockets (best druggability 0.82). MolNFT v1 #105918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RJE
- Type
- protein
- Length
- 1,455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate oxidase
- EC
- 1.13.12.4
- UniProt
- Q44467
- Ligands
- FNR, PYR
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate oxidase (EC 1.13.12.4) | protein | 367 | 44% helix, 13% strand | Q44467 |
| B | Lactate oxidase (EC 1.13.12.4) | protein | 362 | 44% helix, 14% strand | Q44467 |
| C | Lactate oxidase (EC 1.13.12.4) | protein | 361 | 43% helix, 12% strand | Q44467 |
| D | Lactate oxidase (EC 1.13.12.4) | protein | 365 | 44% helix, 13% strand | Q44467 |
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 · 4 copies · chains A, B, C, D
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.82 | 0.98 | 35 | FNR, PYR |
| 2 | 168 | 0.81 | 0.97 | 33 | FNR, PYR |
| 3 | 327 | 0.81 | 0.91 | 64 | FNR, PYR, EDO |
| 4 | 284 | 0.79 | 0.90 | 48 | FNR, PYR, EDO |
| 5 | 90 | 0.60 | 0.88 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1794 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1784 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1782 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1779 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4RJE · Aerococcus viridans L-lactate oxidase mutant · 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 Q44467
- Elsewhere: RCSB PDB 4RJE · PDBe 4RJE · UniProt Q44467
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