MolNFT v1 · #66342 · protein
Crystal structure of the zn-induced tetramer of the engineered cyt CB562 variant ridc-1
3HNI · Soluble cytochrome B562: “Crystal structure of the zn-induced tetramer of the engineered cyt CB562 variant ridc-1”. X-ray diffraction, 2 ligands (HEM, ZN), 14 pockets (best druggability 0.89). MolNFT v1 #66342 on GenesisL1: 3D…
- PDB
- 3HNI
- Type
- protein
- Length
- 848 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, ZN
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, F, D, E, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, C, D, B, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.89 | 0.91 | 100 | empty |
| 2 | 1138 | 0.89 | 0.91 | 116 | HEM |
| 3 | 586 | 0.83 | 0.88 | 68 | HEM |
| 4 | 94 | 0.65 | 0.90 | 21 | empty |
| 5 | 119 | 0.62 | 0.86 | 22 | HEM |
Interfaces
15 interfaces between chains.
- E–F · 784 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 780 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 755 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 725 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 563 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (heme attachment).
Compared structures
- 3HNI · Crystal structure of the Zn-induced tetramer of the engineered cyt cb562 variant RIDC-1 · the same entry in another collection · chain H against H, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain F 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 3HNI · PDBe 3HNI · UniProt P0ABE7
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