Research workbench
Crystal structure of VAO-type flavoprotein MtVAO713 from Myceliophthora thermophila C1
Analyse Crystal structure of VAO-type flavoprotein MtVAO713 from Myceliophthora… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F74
- Type
- protein
- Length
- 2,287 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799)
- Molecule
- Alcohol oxidase
- UniProt
- G2QMS8
- Ligands
- FAD, NAG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Alcohol oxidase | protein | 572 | 33% helix, 21% strand | G2QMS8 |
| C | Alcohol oxidase | protein | 571 | 33% helix, 21% strand | G2QMS8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.86 | 0.87 | 109 | FAD |
| 2 | 641 | 0.85 | 0.90 | 69 | FAD |
| 3 | 904 | 0.83 | 0.84 | 80 | FAD |
| 4 | 839 | 0.82 | 0.84 | 79 | FAD |
| 5 | 571 | 0.75 | 0.82 | 60 | empty |
Interfaces
5 interfaces between chains.
- B–D · 575 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 507 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 436 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 8 glycan, 4 cofactor (disulfide, N-glycosylation, flavinylation).
Compared structures
- 6F74 · Crystal structure of vao-type flavoprotein MTVAO713 from myceliophthora thermophila C1 · 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 G2QMS8
- Elsewhere: RCSB PDB 6F74 · PDBe 6F74 · UniProt G2QMS8
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