MolNFT v1 · #179201 · protein
Binary soak structure of alkanesulfonate monooxygenase msud from pseudomonas fluorescens with FMN
7JYB: “Binary soak structure of alkanesulfonate monooxygenase msud from pseudomonas fluorescens with FMN”. X-ray diffraction, 2 ligands (FMN, PO4), 20 pockets (best druggability 0.87). MolNFT v1 #179201 on GenesisL1: 3D structure, binding…
- PDB
- 7JYB
- Type
- protein
- Length
- 2,715 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkanesulfonate monooxygenase
- EC
- 1.14.14.5
- UniProt
- Q3K9A1
- Ligands
- FMN, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkanesulfonate monooxygenase (EC 1.14.14.5) | protein | 357 | 42% helix, 18% strand | Q3K9A1 |
| B | Alkanesulfonate monooxygenase (EC 1.14.14.5) | protein | 327 | 40% helix, 20% strand | Q3K9A1 |
| C, E | Alkanesulfonate monooxygenase (EC 1.14.14.5) | protein | 356 | 42% helix, 19% strand | Q3K9A1 |
| D | Alkanesulfonate monooxygenase (EC 1.14.14.5) | protein | 326 | 40% helix, 21% strand | Q3K9A1 |
| F | Alkanesulfonate monooxygenase (EC 1.14.14.5) | protein | 323 | 41% helix, 21% strand | Q3K9A1 |
| G | Alkanesulfonate monooxygenase (EC 1.14.14.5) | protein | 322 | 40% helix, 21% strand | Q3K9A1 |
| H | Alkanesulfonate monooxygenase (EC 1.14.14.5) | protein | 348 | 39% helix, 20% strand | Q3K9A1 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, G
- PO4 · Phosphate ion · ion · 2 copies · chains F, H
- SIN · Succinic acid · additive · chains E
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 | 429 | 0.87 | 0.95 | 52 | FMN, SIN |
| 2 | 650 | 0.83 | 0.87 | 54 | empty |
| 3 | 956 | 0.82 | 0.84 | 84 | empty |
| 4 | 674 | 0.81 | 0.85 | 56 | empty |
| 5 | 769 | 0.80 | 0.84 | 83 | FMN |
Interfaces
12 interfaces between chains.
- C–D · 2019 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2015 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2014 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1979 Ų buried · 24 hydrogen bonds · protein-protein
- E–H · 1572 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7JYB · Binary soak structure of alkanesulfonate monooxygenase MsuD from Pseudomonas fluorescens… · 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 Q3K9A1
- Elsewhere: RCSB PDB 7JYB · PDBe 7JYB · UniProt Q3K9A1
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