MolNFT v1 · #70870 · protein
Crystal structure of [2FE-2S] ferredoxin arx from novosphingobium aromaticivorans
3LXF: “Crystal structure of [2FE-2S] ferredoxin arx from novosphingobium aromaticivorans”. X-ray diffraction, 1 ligand (FES), 5 pockets (best druggability 0.61). MolNFT v1 #70870 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3LXF
- Type
- protein
- Length
- 520 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin
- UniProt
- Q2G8A3
- Ligands
- FES
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Ferredoxin | protein | 104 | 26% helix, 22% strand | Q2G8A3 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.61 | 0.89 | 21 | empty |
| 2 | 77 | 0.59 | 0.89 | 23 | empty |
| 3 | 74 | 0.56 | 0.88 | 22 | empty |
| 4 | 77 | 0.53 | 0.86 | 21 | empty |
| 5 | 69 | 0.53 | 0.87 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–C · 434 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 420 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 418 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 416 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 409 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3LXF · Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans · 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 Q2G8A3
- Elsewhere: RCSB PDB 3LXF · PDBe 3LXF · UniProt Q2G8A3
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