MolNFT v1 · #146451 · protein
Crystallogrpahic tetramer of zn-bound RIDC1 variant bearing two disulfide bonded cysteines
6DHY · Soluble cytochrome B562: “Crystallogrpahic tetramer of zn-bound RIDC1 variant bearing two disulfide bonded cysteines”. X-ray diffraction, 3 ligands (HEC, ZN, CA), 7 pockets (best druggability 0.89). MolNFT v1 #146451 on GenesisL1…
- PDB
- 6DHY
- 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, CA
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome B562 | protein | 106 | 74% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 10 copies · chains A, C, D, B
- CA · Calcium ion · metal · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.89 | 0.93 | 99 | empty |
| 2 | 136 | 0.59 | 0.83 | 21 | HEC |
| 3 | 137 | 0.58 | 0.83 | 23 | HEC |
| 4 | 155 | 0.57 | 0.81 | 23 | HEC |
| 5 | 156 | 0.56 | 0.81 | 21 | HEC |
Interfaces
6 interfaces between chains.
- A–D · 800 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 711 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 577 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 570 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 264 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 disulfide (heme c attachment, disulfide).
Compared structures
- 6DHY · Crystallogrpahic tetramer of Zn-bound RIDC1 variant bearing two disulfide bonded cysteines · 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 6DHY · PDBe 6DHY · UniProt P0ABE7
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