MolNFT v1 · #127616 · protein
Crystal structure of complex between flavocytochrome C and copper chaperone copc from T. paradoxus
5N1T · Flavin-binding subunit of sulfide dehydrogenase: “Crystal structure of complex between flavocytochrome C and copper chaperone copc from T. paradoxus”. X-ray diffraction, 3 ligands (FAD, HEC, CU), 6 pockets (best druggability 0.78).…
- PDB
- 5N1T
- Type
- protein
- Length
- 716 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin-binding subunit of sulfide dehydrogenase; Cytochrome C; Copc
- UniProt
- W0DP88, W0DKT4, W0DSL1
- Ligands
- FAD, HEC, CU
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavin-binding subunit of sulfide dehydrogenase | protein | 393 | 31% helix, 27% strand | W0DP88 |
| B | Cytochrome C | protein | 75 | 64% helix, 0% strand | W0DKT4 |
| M | Copc | protein | 124 | 7% helix, 42% strand | W0DSL1 |
| W | Copc | protein | 124 | 6% helix, 48% strand | W0DSL1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- HEC · Heme C · ligand · chains A, B
- CU · Copper (II) ion · metal · chains W
- GOL · Glycerol · additive · chains W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.78 | 0.86 | 54 | FAD |
| 2 | 203 | 0.68 | 0.85 | 30 | HEC |
| 3 | 481 | 0.67 | 0.79 | 64 | empty |
| 4 | 95 | 0.41 | 0.78 | 22 | empty |
| 5 | 120 | 0.41 | 0.75 | 31 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1422 Ų buried · 19 hydrogen bonds · protein-protein
- M–W · 810 Ų buried · 21 hydrogen bonds · protein-protein
- A–W · 474 Ų buried · 9 hydrogen bonds · protein-protein
- A–M · 179 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 1 modified (heme c attachment, flavinylation, oxidation).
Compared structures
- 5N1T · Crystal structure of complex between flavocytochrome c and copper chaperone CopC from T.… · 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 W0DP88
- Every structure of UniProt W0DKT4
- Every structure of UniProt W0DSL1
- Elsewhere: RCSB PDB 5N1T · PDBe 5N1T · UniProt W0DP88 · UniProt W0DKT4 · UniProt W0DSL1
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