MolNFT v1 · #107406 · protein
Crystal structure of the zn-directed tetramer of the engineered cyt CB562 variant, AB3
4U9D · Soluble cytochrome B562: “Crystal structure of the zn-directed tetramer of the engineered cyt CB562 variant, AB3”. X-ray diffraction, 2 ligands (HEC, ZN), 9 pockets (best druggability 0.89). MolNFT v1 #107406 on GenesisL1: 3D…
- PDB
- 4U9D
- 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
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome B562 | protein | 106 | 77% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.89 | 0.92 | 90 | empty |
| 2 | 182 | 0.58 | 0.81 | 24 | HEC |
| 3 | 126 | 0.58 | 0.84 | 22 | HEC |
| 4 | 130 | 0.57 | 0.83 | 22 | HEC |
| 5 | 70 | 0.57 | 0.89 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 697 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 675 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 670 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 640 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 274 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 4U9D · Crystal Structure of the Zn-directed tetramer of the engineered cyt cb562 variant, AB3 · the same entry in another collection · chain C against C, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A 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 4U9D · PDBe 4U9D · UniProt P0ABE7
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