MolNFT v1 · #59707 · protein
Tetrameric cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) assembly stabilized by interprotein zinc coordination
3C63 · Soluble cytochrome B562: “Tetrameric cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) assembly stabilized by interprotein zinc…”. X-ray diffraction, 3 ligands (HEM, CA, ZN), 9 pockets (best druggability 0.86). MolNFT v1 #59707 on…
- PDB
- 3C63
- 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, CA, ZN
- Pockets
- 9 · best druggability 0.86
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
- CA · Calcium ion · metal · 5 copies · chains A, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.86 | 0.87 | 113 | empty |
| 2 | 176 | 0.71 | 0.89 | 30 | HEM |
| 3 | 67 | 0.66 | 0.93 | 18 | empty |
| 4 | 98 | 0.65 | 0.90 | 21 | empty |
| 5 | 122 | 0.64 | 0.88 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 644 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 554 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 554 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 96 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme attachment).
Compared structures
- 3C63 · Tetrameric Cytochrome cb562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized by… · 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 0.97
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 3C63 · PDBe 3C63 · UniProt P0ABE7
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