MolNFT v1 · #90166 · protein
A. fulgidus iscs-iscu complex structure
4EB7 · Probable cysteine desulfurase 2: “A. fulgidus iscs-iscu complex structure”. X-ray diffraction, 2 ligands (PLP, FES), 6 pockets (best druggability 0.83). MolNFT v1 #90166 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4EB7
- Type
- protein
- Length
- 890 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable cysteine desulfurase 2; Nifu protein (nifu-1)
- EC
- 2.8.1.7
- UniProt
- O29689, O34393
- Ligands
- PLP, FES
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable cysteine desulfurase 2 (EC 2.8.1.7) | protein | 378 | 42% helix, 17% strand | O29689 |
| B | Probable cysteine desulfurase 2 (EC 2.8.1.7) | protein | 377 | 44% helix, 16% strand | O29689 |
| C | Nifu protein (nifu-1) | protein | 135 | 47% helix, 18% strand | O34393 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.83 | 0.86 | 75 | PLP |
| 2 | 802 | 0.82 | 0.85 | 77 | PLP, GOL |
| 3 | 170 | 0.65 | 0.85 | 21 | GOL |
| 4 | 346 | 0.63 | 0.79 | 49 | FES |
| 5 | 63 | 0.35 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2127 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 739 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 O29689
- Every structure of UniProt O34393
- Elsewhere: RCSB PDB 4EB7 · PDBe 4EB7 · UniProt O29689 · UniProt O34393
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