MolNFT v1 · #169057 · protein
Ni-bound structure of an engineered metal-dependent protein trimer, TRICYT1
6WZA · Soluble cytochrome B562: “Ni-bound structure of an engineered metal-dependent protein trimer, TRICYT1”. X-ray diffraction, 4 ligands (HEC, NA, NI), 9 pockets (best druggability 0.84). MolNFT v1 #169057 on GenesisL1: 3D structure…
- PDB
- 6WZA
- 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, NA, NI, CL
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Soluble cytochrome B562 | protein | 106 | 80% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 5 copies · chains A, B, C
- NI · Nickel (II) ion · metal · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.84 | 0.93 | 38 | NA, CL |
| 2 | 140 | 0.58 | 0.83 | 25 | HEC, MPD |
| 3 | 142 | 0.58 | 0.82 | 22 | HEC |
| 4 | 148 | 0.58 | 0.82 | 21 | HEC |
| 5 | 204 | 0.52 | 0.77 | 29 | CL |
Interfaces
3 interfaces between chains.
- A–C · 564 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 548 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (heme c attachment).
Compared structures
- 6WZA · Ni-bound structure of an engineered metal-dependent protein trimer, TriCyt1 · 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 B 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 6WZA · PDBe 6WZA · UniProt P0ABE7
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