MolNFT v1 · #165317 · protein
Native cytochrome C6 from thermosynechococcus elongatus in space group H3
6TR1: “Native cytochrome C6 from thermosynechococcus elongatus in space group H3”. X-ray diffraction, 2 ligands (HEC, NA), 4 pockets (best druggability 0.73). MolNFT v1 #165317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TR1
- Type
- protein
- Length
- 259 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C6
- UniProt
- P0A3X9
- Ligands
- HEC, NA
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C6 | protein | 86 | 59% helix, 3% strand | P0A3X9 |
| C | Cytochrome C6 | protein | 87 | 59% helix, 2% strand | P0A3X9 |
| E | Cytochrome C6 | protein | 86 | 59% helix, 3% strand | P0A3X9 |
Ligands and binding sites
- HEC · Heme C · ligand · 3 copies · chains A, C, E
- NA · Sodium ion · metal · 5 copies · chains A, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.73 | 0.88 | 30 | HEC |
| 2 | 221 | 0.71 | 0.86 | 29 | HEC |
| 3 | 207 | 0.70 | 0.87 | 31 | HEC |
| 4 | 270 | 0.63 | 0.80 | 23 | NA |
Interfaces
2 interfaces between chains.
- A–C · 453 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 182 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 cofactor, 1 modified (heme c attachment, nonstandard).
Compared structures
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 P0A3X9
- Elsewhere: RCSB PDB 6TR1 · PDBe 6TR1 · UniProt P0A3X9
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