MolNFT v1 · #23415 · protein
Crystal structure of pyranose 2-oxidase from the white-rot fungus peniophora sp.
1TZL · Pyranose oxidase: “Crystal structure of pyranose 2-oxidase from the white-rot fungus peniophora sp.”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.89). MolNFT v1 #23415 on GenesisL1: 3D structure, binding sites…
- PDB
- 1TZL
- Type
- protein
- Length
- 4,616 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyranose oxidase
- EC
- 1.1.3.10
- UniProt
- Q8J136
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Pyranose oxidase (EC 1.1.3.10) | protein | 577 | 25% helix, 23% strand | Q8J136 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.89 | 0.94 | 66 | FAD |
| 2 | 1194 | 0.88 | 0.90 | 131 | FAD |
| 3 | 586 | 0.88 | 0.94 | 70 | FAD |
| 4 | 561 | 0.88 | 0.94 | 63 | FAD |
| 5 | 578 | 0.88 | 0.93 | 76 | FAD |
Interfaces
14 interfaces between chains.
- B–D · 2815 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2784 Ų buried · 42 hydrogen bonds · protein-protein
- E–G · 2784 Ų buried · 44 hydrogen bonds · protein-protein
- F–H · 2755 Ų buried · 43 hydrogen bonds · protein-protein
- F–G · 1210 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 128 modified, 8 cofactor (engineered, flavinylation).
Compared structures
- 1TZL · Crystal Structure of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp. · the same entry in another collection · chain H against H, TM-score 1.00
- Q8J136 · AlphaFold monomer V2.0 prediction for pyranose 2-oxidase (Q8J136) · 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 Q8J136
- Elsewhere: RCSB PDB 1TZL · PDBe 1TZL · UniProt Q8J136
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