MolNFT v1 · #139898 · protein
Crystal structure of baculoviral sulfhydryl oxidase P33 (H227A mutant)
5XTP · FAD-linked sulfhydryl oxidase: “Crystal structure of baculoviral sulfhydryl oxidase P33 (H227A mutant)”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.76). MolNFT v1 #139898 on GenesisL1: 3D structure, binding…
- PDB
- 5XTP
- Type
- protein
- Length
- 977 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-linked sulfhydryl oxidase
- EC
- 1.8.3.2
- UniProt
- P41480
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-linked sulfhydryl oxidase (EC 1.8.3.2) | protein | 240 | 69% helix, 3% strand | P41480 |
| B | FAD-linked sulfhydryl oxidase (EC 1.8.3.2) | protein | 239 | 71% helix, 3% strand | P41480 |
| C | FAD-linked sulfhydryl oxidase (EC 1.8.3.2) | protein | 249 | 69% helix, 2% strand | P41480 |
| D | FAD-linked sulfhydryl oxidase (EC 1.8.3.2) | protein | 249 | 70% helix, 2% strand | P41480 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.76 | 0.93 | 29 | empty |
| 2 | 1106 | 0.76 | 0.78 | 78 | empty |
| 3 | 1045 | 0.75 | 0.78 | 100 | FAD |
| 4 | 168 | 0.75 | 0.92 | 30 | empty |
| 5 | 207 | 0.72 | 0.88 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1764 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1759 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 405 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 231 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5XTP · Crystal structure of baculoviral sulfhydryl oxidase P33 (H227A 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 P41480
- Elsewhere: RCSB PDB 5XTP · PDBe 5XTP · UniProt P41480
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