MolNFT v1 · #12623 · protein
E. COLI NIFS/CSDB protein at 2.0A with the cysteine persulfide intermediate (residue css).
1KMJ · Selenocysteine lyase: “E. COLI NIFS/CSDB protein at 2.0A with the cysteine persulfide intermediate (residue css).”. X-ray diffraction, 1 ligand (PLP), 2 pockets (best druggability 0.51). MolNFT v1 #12623 on GenesisL1: 3D structure…
- PDB
- 1KMJ
- Type
- protein
- Length
- 405 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenocysteine lyase
- EC
- 4.4.1.16
- UniProt
- P77444
- Ligands
- PLP
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenocysteine lyase (EC 4.4.1.16) | protein | 405 | 44% helix, 19% strand | P77444 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
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 | 137 | 0.51 | 0.80 | 28 | empty |
| 2 | 98 | 0.44 | 0.79 | 28 | PLP |
Modifications
Observed in the structure: 1 cofactor, 1 modified (pyridoxal phosphate Schiff base, oxidation).
Compared structures
- 1KMJ · E. coli NifS/CsdB protein at 2.0A with the cysteine persulfide intermediate (residue CSS). · the same entry in another collection · chain A against A, TM-score 1.00
- P77444 · AlphaFold monomer V2.0 prediction for cysteine desulfurase (P77444) · a predicted model of the same protein · 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
- Every structure of UniProt P77444
- Elsewhere: RCSB PDB 1KMJ · PDBe 1KMJ · UniProt P77444
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