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Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide bonded cysteines
Analyse Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DHZ
- Type
- protein
- Length
- 410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEC, CA
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Soluble cytochrome B562 | protein | 106 | 82% helix, 0% strand | P0ABE7 |
| C | Soluble cytochrome B562 | protein | 99 | 84% helix, 0% strand | P0ABE7 |
| D | Soluble cytochrome B562 | protein | 99 | 83% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 7 copies · chains A, B, C, D
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 | 571 | 0.67 | 0.77 | 67 | HEC |
| 2 | 167 | 0.60 | 0.82 | 24 | HEC |
| 3 | 168 | 0.59 | 0.82 | 28 | HEC |
| 4 | 139 | 0.54 | 0.81 | 20 | empty |
| 5 | 161 | 0.51 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–D · 674 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 648 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 167 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor, 3 disulfide (heme c attachment, disulfide).
Compared structures
- 6DHZ · Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide bonded… · 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 A against A, TM-score 0.98
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 6DHZ · PDBe 6DHZ · UniProt P0ABE7
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