Research workbench
Crystal structure of the zn-induced tetramer of the engineered cyt CB562 variant ridc-2
Analyse Crystal structure of the zn-induced tetramer of the engineered cyt CB562… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HNJ
- 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
- HEM, ZN
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, C, D, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.88 | 0.89 | 100 | empty |
| 2 | 152 | 0.59 | 0.83 | 21 | HEM |
| 3 | 178 | 0.59 | 0.81 | 24 | HEM |
| 4 | 154 | 0.58 | 0.82 | 24 | HEM |
| 5 | 154 | 0.55 | 0.81 | 26 | HEM |
Interfaces
6 interfaces between chains.
- B–C · 800 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 792 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 511 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 466 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 262 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 cofactor (heme attachment).
Compared structures
- 3HNJ · Crystal structure of the Zn-induced tetramer of the engineered cyt cb562 variant RIDC-2 · 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 D 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 3HNJ · PDBe 3HNJ · UniProt P0ABE7
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