MolNFT v1 · #169626 · protein
X-ray crystal structure of mqne from pedobacter heparinus in complex with aminofutalosine and methionine
6XI9 · Aminodeoxyfutalosine synthase: “X-ray crystal structure of mqne from pedobacter heparinus in complex with aminofutalosine and methionine”. X-ray diffraction, 4 ligands (SF4, MET, V47), 11 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6XI9
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminodeoxyfutalosine synthase
- EC
- 2.5.1.120
- UniProt
- C6XW09
- Ligands
- SF4, MET, V47, CL
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminodeoxyfutalosine synthase (EC 2.5.1.120) | protein | 380 | 46% helix, 14% strand | C6XW09 |
| B | Aminodeoxyfutalosine synthase (EC 2.5.1.120) | protein | 380 | 44% helix, 14% strand | C6XW09 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- MET · Methionine · ligand · 2 copies · chains A, B
- V47 · 9-[7-(3-carboxyphenyl)-5,6-dideoxy-beta-D-ribo-heptodialdo-1,4-furanosyl]-9H-purin-6-amine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.78 | 0.83 | 45 | SF4, MET, V47, CL |
| 2 | 865 | 0.78 | 0.81 | 77 | empty |
| 3 | 723 | 0.75 | 0.80 | 53 | SF4, MET, V47 |
| 4 | 178 | 0.52 | 0.78 | 24 | empty |
| 5 | 91 | 0.45 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 772 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6XI9 · X-ray crystal structure of MqnE from Pedobacter heparinus in complex with aminofutalosine… · 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 C6XW09
- Elsewhere: RCSB PDB 6XI9 · PDBe 6XI9 · UniProt C6XW09
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