MolNFT v1 · #165363 · protein
Cytochrome C6 from thermosynechococcus elongatus in a monoclinic space group
6TSY: “Cytochrome C6 from thermosynechococcus elongatus in a monoclinic space group”. X-ray diffraction, 2 ligands (HEC, SO4), 6 pockets (best druggability 0.84). MolNFT v1 #165363 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6TSY
- Type
- protein
- Length
- 515 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C6
- UniProt
- P0A3X9
- Ligands
- HEC, SO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Cytochrome C6 | protein | 86 | 58% helix, 5% strand | P0A3X9 |
| B | Cytochrome C6 | protein | 87 | 54% helix, 2% strand | P0A3X9 |
| C, E | Cytochrome C6 | protein | 85 | 60% helix, 2% strand | P0A3X9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.84 | 0.87 | 93 | HEC |
| 2 | 478 | 0.83 | 0.89 | 62 | HEC |
| 3 | 257 | 0.75 | 0.88 | 36 | HEC |
| 4 | 232 | 0.73 | 0.87 | 31 | HEC |
| 5 | 83 | 0.34 | 0.75 | 24 | empty |
Interfaces
12 interfaces between chains.
- B–D · 526 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 464 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 456 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 339 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 327 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 cofactor (heme c attachment).
Compared structures
- 6TSY · Cytochrome c6 from Thermosynechococcus elongatus in a monoclinic space group · the same entry in another collection · chain F against F, TM-score 1.00
- P0A3X9 · AlphaFold monomer V2.0 prediction for cytochrome C6 (P0A3X9) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 6TSY · PDBe 6TSY · UniProt P0A3X9
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