MolNFT v1 · #58174 · protein
Refined structure of plant-type [2FE-2S] ferredoxin I from aphanothece sacrum at 1.46 a resolution
3AV8 · Ferredoxin-1: “Refined structure of plant-type [2FE-2S] ferredoxin I from aphanothece sacrum at 1.46 a resolution”. X-ray diffraction, 2 ligands (FES, SO4), 2 pockets (best druggability 0.65). MolNFT v1 #58174 on GenesisL1: 3D…
- PDB
- 3AV8
- Type
- protein
- Length
- 388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin-1
- Ligands
- FES, SO4
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ferredoxin-1 | protein | 97 | 20% helix, 30% strand | — |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.65 | 0.76 | 60 | empty |
| 2 | 100 | 0.37 | 0.75 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–D · 358 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 115 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3AV8 · Refined Structure of Plant-type [2Fe-2S] Ferredoxin I from Aphanothece sacrum at 1.46 A… · 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
- Elsewhere: RCSB PDB 3AV8 · PDBe 3AV8
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