MolNFT v1 · #104060 · protein
Berberine bridge enzyme G164A variant, a reticuline dehydrogenase
4PZF · Reticuline oxidase: “Berberine bridge enzyme G164A variant, a reticuline dehydrogenase”. X-ray diffraction, 3 ligands (FAD, NAG, SO4), 18 pockets (best druggability 0.86). MolNFT v1 #104060 on GenesisL1: 3D structure, binding sites…
- PDB
- 4PZF
- Type
- protein
- Length
- 1,989 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticuline oxidase
- EC
- 1.21.3.3
- UniProt
- P30986
- Ligands
- FAD, NAG, SO4
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticuline oxidase (EC 1.21.3.3) | protein | 498 | 36% helix, 20% strand | P30986 |
| B | Reticuline oxidase (EC 1.21.3.3) | protein | 498 | 37% helix, 21% strand | P30986 |
| C | Reticuline oxidase (EC 1.21.3.3) | protein | 496 | 38% helix, 21% strand | P30986 |
| D | Reticuline oxidase (EC 1.21.3.3) | protein | 497 | 36% helix, 21% strand | P30986 |
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
- SO4 · Sulfate ion · ion · 5 copies · chains B, D, A, C
- 12P · Dodecaethylene glycol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.86 | 0.88 | 89 | FAD |
| 2 | 909 | 0.86 | 0.87 | 90 | FAD |
| 3 | 954 | 0.86 | 0.87 | 88 | FAD |
| 4 | 953 | 0.85 | 0.86 | 94 | FAD |
| 5 | 605 | 0.67 | 0.77 | 65 | SO4, 12P |
Interfaces
4 interfaces between chains.
- A–C · 697 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 691 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 518 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 8 glycan, 4 disulfide (flavinylation, N-glycosylation, disulfide).
Compared structures
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 P30986
- Elsewhere: RCSB PDB 4PZF · PDBe 4PZF · UniProt P30986
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