MolNFT v1 · #118884 · protein
[2FE:2S] ferredoxin fesii from azotobacter vinelandii
5FFI · Dimeric (2FE-2S) protein: “[2FE:2S] ferredoxin fesii from azotobacter vinelandii”. X-ray diffraction, 1 ligand (FES), 9 pockets (best druggability 0.81). MolNFT v1 #118884 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5FFI
- Type
- protein
- Length
- 569 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimeric (2FE-2S) protein
- UniProt
- Q44501
- Ligands
- FES
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimeric (2FE-2S) protein | protein | 118 | 22% helix, 23% strand | Q44501 |
| B | Dimeric (2FE-2S) protein | protein | 116 | 22% helix, 25% strand | Q44501 |
| C | Dimeric (2FE-2S) protein | protein | 116 | 22% helix, 23% strand | Q44501 |
| D | Dimeric (2FE-2S) protein | protein | 117 | 24% helix, 23% strand | Q44501 |
| E | Dimeric (2FE-2S) protein | protein | 102 | 19% helix, 28% strand | Q44501 |
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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.81 | 0.85 | 90 | empty |
| 2 | 213 | 0.59 | 0.81 | 30 | empty |
| 3 | 143 | 0.58 | 0.83 | 28 | empty |
| 4 | 79 | 0.46 | 0.82 | 14 | empty |
| 5 | 140 | 0.45 | 0.76 | 25 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1273 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1256 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 519 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 383 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 193 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q44501
- Elsewhere: RCSB PDB 5FFI · PDBe 5FFI · UniProt Q44501
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