MolNFT v1 · #146976 · protein
Vanadyl-bound structure of the engineered cyt B562 variant, CH3Y*
6DYL · Soluble cytochrome B562: “Vanadyl-bound structure of the engineered cyt B562 variant, CH3Y*”. X-ray diffraction, 1 ligand (V), 6 pockets (best druggability 0.66). MolNFT v1 #146976 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DYL
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- V
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Soluble cytochrome B562 | protein | 106 | 81% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- V · Vanadium ion · metal · 2 copies · chains A, E, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.66 | 0.81 | 28 | empty |
| 2 | 283 | 0.63 | 0.80 | 32 | empty |
| 3 | 299 | 0.58 | 0.77 | 38 | empty |
| 4 | 95 | 0.47 | 0.80 | 16 | empty |
| 5 | 163 | 0.45 | 0.75 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–E · 570 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 529 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 429 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6DYL · Vanadyl-bound structure of the engineered cyt b562 variant, CH3Y* · the same entry in another collection · chain G against G, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 6DYL · PDBe 6DYL · UniProt P0ABE7
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