MolNFT v1 · #169041 · protein
Crystallographic trimer of metal-free TRICYT2
6WYU · Soluble cytochrome B562: “Crystallographic trimer of metal-free TRICYT2”. X-ray diffraction, 2 ligands (HEC, SO4), 8 pockets (best druggability 0.73). MolNFT v1 #169041 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WYU
- 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, SO4
- Pockets
- 8 · best druggability 0.73
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
- SO4 · Sulfate ion · ion · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.98 | 15 | SO4 |
| 2 | 264 | 0.58 | 0.78 | 34 | empty |
| 3 | 141 | 0.57 | 0.82 | 22 | HEC |
| 4 | 126 | 0.55 | 0.82 | 20 | HEC |
| 5 | 135 | 0.55 | 0.81 | 22 | HEC |
Interfaces
3 interfaces between chains.
- A–B · 633 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 629 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 590 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (heme c attachment).
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 P0ABE7
- Elsewhere: RCSB PDB 6WYU · PDBe 6WYU · UniProt P0ABE7
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