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Structure of a catalytically inactive mutant (K223A) of C-des with a substrate (cystine) linked to the co-factor
Analyse Structure of a catalytically inactive mutant (K223A) of C-des with a substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N31
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-CYSTEINE/CYSTINE lyase C-des
- EC
- 4.4.1.-
- Ligands
- CYS, PLP, K
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-CYSTEINE/CYSTINE lyase C-des (EC 4.4.1.-) | protein | 386 | 41% helix, 18% strand | — |
Ligands and binding sites
- CYS · Cysteine · ligand · 4 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.82 | 0.98 | 32 | empty |
| 2 | 681 | 0.76 | 0.81 | 71 | CYS, PLP |
| 3 | 674 | 0.75 | 0.81 | 70 | PLP, CYS |
| 4 | 73 | 0.54 | 0.86 | 20 | empty |
| 5 | 70 | 0.48 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3020 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 1N31 · Structure of A Catalytically Inactive Mutant (K223A) of C-DES with a Substrate (Cystine)… · 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
- Elsewhere: RCSB PDB 1N31 · PDBe 1N31
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