MolNFT v1 · #148454 · protein
Crystal structure of vao-type flavoprotein MTVAO615 at pH 5.0 from myceliophthora thermophila C1
6F73: “Crystal structure of vao-type flavoprotein MTVAO615 at pH 5.0 from myceliophthora thermophila C1”. X-ray diffraction, 2 ligands (FAD, NAG), 5 pockets (best druggability 0.84). MolNFT v1 #148454 on GenesisL1: 3D structure, binding…
- PDB
- 6F73
- Type
- protein
- Length
- 1,096 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MTVAO615
- UniProt
- G2QDQ9
- Ligands
- FAD, NAG
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MTVAO615 | protein | 548 | 36% helix, 22% strand | G2QDQ9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.84 | 0.90 | 57 | FAD |
| 2 | 488 | 0.83 | 0.89 | 57 | FAD |
| 3 | 1171 | 0.81 | 0.82 | 98 | empty |
| 4 | 200 | 0.55 | 0.79 | 28 | empty |
| 5 | 188 | 0.52 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 485 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 8 disulfide, 4 cofactor (N-glycosylation, disulfide, flavinylation).
Compared structures
- 6F73 · Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 from Myceliophthora… · the same entry in another collection · chain A against A, TM-score 1.00
- G2QDQ9 · AlphaFold monomer V2.0 prediction for vao-type flavoprotein oxidase VAO615 (G2QDQ9) · a predicted model of the same protein · 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 G2QDQ9
- Elsewhere: RCSB PDB 6F73 · PDBe 6F73 · UniProt G2QDQ9
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