MolNFT v1 · #155165 · protein
CU(II) complex of hocl-induced flavoprotein disulfide reductase rcla from escherichia COLI
6KYY · Pyridine nucleotide-disulphide oxidoreductase dimerisation…: “CU(II) complex of hocl-induced flavoprotein disulfide reductase rcla from escherichia COLI”. X-ray diffraction, 3 ligands (FAD, CU, CL), 12 pockets (best druggability…
- PDB
- 6KYY
- Type
- protein
- Length
- 1,753 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
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridine nucleotide-disulphide oxidoreductase dimerisation region | protein | 432 | 33% helix, 23% strand | A0A140ND83 |
| B, C | Pyridine nucleotide-disulphide oxidoreductase dimerisation region | protein | 441 | 34% helix, 24% strand | A0A140ND83 |
| D | Pyridine nucleotide-disulphide oxidoreductase dimerisation region | protein | 439 | 31% helix, 23% strand | A0A140ND83 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 32 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.85 | 0.86 | 137 | FAD, CL |
| 2 | 1011 | 0.81 | 0.82 | 106 | FAD |
| 3 | 827 | 0.79 | 0.82 | 96 | FAD, CL |
| 4 | 456 | 0.78 | 0.86 | 49 | CU |
| 5 | 741 | 0.78 | 0.82 | 88 | FAD |
Interfaces
3 interfaces between chains.
- C–D · 2374 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2349 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 851 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6KYY · Cu(II) complex of HOCl-induced flavoprotein disulfide reductase RclA from Escherichia coli · 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 6KYY · PDBe 6KYY · UniProt A0A140ND83
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