MolNFT v1 · #114294 · protein
Crystal structure of a cysteine desulfurase from thermococcus onnurineus NA1 in complex with alanine at 1.5 ångström resolution
5B89: “Crystal structure of a cysteine desulfurase from thermococcus onnurineus NA1 in complex with alanine at 1.5…”. X-ray diffraction, 2 ligands (ALA, PLP), 5 pockets (best druggability 0.73). MolNFT v1 #114294 on GenesisL1: 3D…
- PDB
- 5B89
- Type
- protein
- Length
- 802 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase
- EC
- 2.8.1.7
- UniProt
- B6YT87
- Ligands
- ALA, PLP
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase (EC 2.8.1.7) | protein | 400 | 43% helix, 17% strand | B6YT87 |
| B | Cysteine desulfurase (EC 2.8.1.7) | protein | 402 | 43% helix, 17% strand | B6YT87 |
Ligands and binding sites
- ALA · Alanine · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.73 | 0.86 | 46 | ALA, PLP |
| 2 | 347 | 0.73 | 0.85 | 48 | PLP, ALA |
| 3 | 232 | 0.63 | 0.82 | 26 | empty |
| 4 | 127 | 0.45 | 0.77 | 24 | empty |
| 5 | 50 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3591 Ų buried · 72 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 modified (pyridoxal phosphate Schiff base, oxidation).
Compared structures
- 5B89 · Crystal structure of a Cysteine Desulfurase from Thermococcus onnurineus NA1 in complex… · the same entry in another collection · 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 B6YT87
- Elsewhere: RCSB PDB 5B89 · PDBe 5B89 · UniProt B6YT87
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