MolNFT v1 · #140087 · protein
Crystal structure of the zn-directed tetramer of the engineered cyt CB562 variant, C96T/AB5
5XZJ · Soluble cytochrome B562: “Crystal structure of the zn-directed tetramer of the engineered cyt CB562 variant, C96T/AB5”. X-ray diffraction, 3 ligands (HEC, ZN, CL), 10 pockets (best druggability 0.84). MolNFT v1 #140087 on GenesisL1…
- PDB
- 5XZJ
- 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
- HEC, ZN, CL
- Pockets
- 10 · 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, D | Soluble cytochrome B562 | protein | 106 | 80% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 14 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.84 | 0.92 | 60 | empty |
| 2 | 155 | 0.76 | 0.93 | 30 | ZN |
| 3 | 121 | 0.72 | 0.93 | 23 | ZN |
| 4 | 117 | 0.72 | 0.93 | 22 | empty |
| 5 | 150 | 0.59 | 0.83 | 23 | HEC |
Interfaces
6 interfaces between chains.
- A–B · 774 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 708 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 503 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 495 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 273 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 5XZJ · Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant… · the same entry in another collection · chain D against D, 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 0.96
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 5XZJ · PDBe 5XZJ · UniProt P0ABE7
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