MolNFT v1 · #169633 · protein
X-ray crystal structure of mqne from pedobacter heparinus
6XIG · Aminodeoxyfutalosine synthase: “X-ray crystal structure of mqne from pedobacter heparinus”. X-ray diffraction, 1 ligand (SF4), 6 pockets (best druggability 0.73). MolNFT v1 #169633 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XIG
- Type
- protein
- Length
- 762 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
- Pockets
- 6 · best druggability 0.73
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 | 379 | 45% helix, 14% strand | C6XW09 |
| B | Aminodeoxyfutalosine synthase (EC 2.5.1.120) | protein | 383 | 45% helix, 15% strand | C6XW09 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- TAR · D(-)-tartaric acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.73 | 0.80 | 52 | SF4, TAR |
| 2 | 702 | 0.73 | 0.79 | 57 | empty |
| 3 | 673 | 0.73 | 0.79 | 58 | SF4, TAR |
| 4 | 60 | 0.42 | 0.82 | 14 | empty |
| 5 | 61 | 0.41 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1001 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6XIG · X-ray crystal structure of MqnE from Pedobacter heparinus · 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 6XIG · PDBe 6XIG · UniProt C6XW09
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