MolNFT v1 · #90164 · protein
A. fulgidus iscs-iscu complex structure
4EB5 · Probable cysteine desulfurase 2: “A. fulgidus iscs-iscu complex structure”. X-ray diffraction, 2 ligands (PLP, FES), 9 pockets (best druggability 0.81). MolNFT v1 #90164 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4EB5
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- 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
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable cysteine desulfurase 2 (EC 2.8.1.7) | protein | 379 | 44% helix, 17% strand | O29689 |
| B | Probable cysteine desulfurase 2 (EC 2.8.1.7) | protein | 377 | 43% helix, 16% strand | O29689 |
| C, D | Nifu protein (nifu-1) | protein | 138 | 48% helix, 19% 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, B, D
- 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.81 | 0.83 | 104 | PLP |
| 2 | 1035 | 0.81 | 0.82 | 94 | PLP |
| 3 | 62 | 0.67 | 0.95 | 17 | GOL |
| 4 | 172 | 0.61 | 0.82 | 19 | GOL |
| 5 | 52 | 0.43 | 0.83 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2102 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 894 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 806 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 45 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 O29689
- Every structure of UniProt O34393
- Elsewhere: RCSB PDB 4EB5 · PDBe 4EB5 · UniProt O29689 · UniProt O34393
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