MolNFT v1 · #12624 · protein
E. COLI NIFS/CSDB protein at 2.20A with the cysteine perselenide intermediate (residue csz).
1KMK · Selenocysteine lyase: “E. COLI NIFS/CSDB protein at 2.20A with the cysteine perselenide intermediate (residue csz).”. X-ray diffraction, 2 ligands (SEC, PLP), 3 pockets (best druggability 0.47). MolNFT v1 #12624 on GenesisL1: 3D…
- PDB
- 1KMK
- 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
- SEC, PLP
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenocysteine lyase (EC 4.4.1.16) | protein | 405 | 43% helix, 19% strand | P77444 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.47 | 0.81 | 18 | empty |
| 2 | 69 | 0.45 | 0.83 | 25 | SEC, PLP |
| 3 | 61 | 0.41 | 0.81 | 14 | empty |
Modifications
Observed in the structure: 1 cofactor, 1 modified (pyridoxal phosphate Schiff base, nonstandard).
Compared structures
- 1KMK · E. coli NifS/CsdB protein at 2.20A with the cysteine perselenide intermediate (residue… · 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 1KMK · PDBe 1KMK · UniProt P77444
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