MolNFT v1 · #142088 · protein
L-cysteine-plp reaction intermediate of nifs from hydrogenimonas thermophila
5ZSS · Cysteine desulfurase: “L-cysteine-plp reaction intermediate of nifs from hydrogenimonas thermophila”. X-ray diffraction, 1 ligand (C6P), 8 pockets (best druggability 0.81). MolNFT v1 #142088 on GenesisL1: 3D structure, binding sites…
- PDB
- 5ZSS
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase
- UniProt
- A0A1I5NEH3
- Ligands
- C6P
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase | protein | 388 | 39% helix, 19% strand | A0A1I5NEH3 |
| B | Cysteine desulfurase | protein | 385 | 40% helix, 19% strand | A0A1I5NEH3 |
Ligands and binding sites
- C6P · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-cysteine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.81 | 0.98 | 24 | empty |
| 2 | 79 | 0.75 | 0.98 | 20 | empty |
| 3 | 482 | 0.70 | 0.80 | 67 | C6P |
| 4 | 408 | 0.63 | 0.78 | 47 | empty |
| 5 | 108 | 0.38 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2603 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 5ZSS · L-Cysteine-PLP reaction intermediate of NifS from Hydrogenimonas thermophila · the same entry in another collection · chain B against B, 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 A0A1I5NEH3
- Elsewhere: RCSB PDB 5ZSS · PDBe 5ZSS · UniProt A0A1I5NEH3
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