MolNFT v1 · #154850 · protein
CU(II) complex of hocl-induced flavoprotein disulfide reductase rcla C43S mutant from escherichia COLI
6KOD · Pyridine nucleotide-disulphide oxidoreductase dimerisation…: “CU(II) complex of hocl-induced flavoprotein disulfide reductase rcla C43S mutant from escherichia COLI”. X-ray diffraction, 3 ligands (FAD, CU, CL), 15 pockets (best…
- PDB
- 6KOD
- Type
- protein
- Length
- 1,763 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridine nucleotide-disulphide oxidoreductase dimerisation region
- UniProt
- A0A140ND83
- Ligands
- FAD, CU, CL
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridine nucleotide-disulphide oxidoreductase dimerisation region | protein | 440 | 34% helix, 25% strand | A0A140ND83 |
| B, C, D | Pyridine nucleotide-disulphide oxidoreductase dimerisation region | protein | 441 | 33% helix, 26% strand | A0A140ND83 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 52 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.82 | 0.83 | 120 | FAD, CL, CU |
| 2 | 742 | 0.79 | 0.83 | 86 | FAD, CU |
| 3 | 683 | 0.77 | 0.82 | 81 | FAD |
| 4 | 618 | 0.77 | 0.83 | 73 | FAD |
| 5 | 405 | 0.75 | 0.85 | 48 | CU |
Interfaces
3 interfaces between chains.
- C–D · 2420 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2411 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 879 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6KOD · Cu(II) complex of HOCl-induced flavoprotein disulfide reductase RclA C43S mutant from… · 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 A0A140ND83
- Elsewhere: RCSB PDB 6KOD · PDBe 6KOD · UniProt A0A140ND83
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.