Research workbench
Fe-bound structure of an engineered metal-dependent protein trimer, TRICYT2
Analyse Fe-bound structure of an engineered metal-dependent protein trimer, TRICYT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WZ0
- Type
- protein
- Length
- 318 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEC, FE2, SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 3 copies · chains A, B, C
- FE2 · Fe (II) ion · metal · chains A, B, C
- SO4 · Sulfate ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.75 | 0.98 | 22 | SO4 |
| 2 | 145 | 0.60 | 0.83 | 22 | HEC |
| 3 | 153 | 0.57 | 0.82 | 24 | HEC |
| 4 | 174 | 0.56 | 0.80 | 28 | HEC |
| 5 | 285 | 0.55 | 0.76 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 617 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 608 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (heme c attachment).
Compared structures
- 6WZ0 · Fe-bound structure of an engineered metal-dependent protein trimer, TriCyt2 · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0ABE7
- Elsewhere: RCSB PDB 6WZ0 · PDBe 6WZ0 · UniProt P0ABE7
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