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Crystal structure of the zn-RIDC1 complex stabilized by bmoe crosslinks cocrystallized in the presence of CU(II)
Analyse Crystal structure of the zn-RIDC1 complex stabilized by bmoe crosslinks… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QVZ
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome CB562
- Ligands
- HEM, ME7, CU, ZN
- Pockets
- 8 · 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 | Cytochrome CB562 | protein | 106 | 79% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- ME7 · 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) · ligand · 2 copies · chains A, C, B, D
- CU · Copper (II) ion · metal · 8 copies · chains A, C
- ZN · Zinc ion · metal · 5 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.89 | 0.90 | 116 | empty |
| 2 | 139 | 0.57 | 0.82 | 23 | HEM |
| 3 | 137 | 0.57 | 0.82 | 22 | HEM |
| 4 | 154 | 0.56 | 0.81 | 22 | HEM |
| 5 | 144 | 0.56 | 0.82 | 24 | HEM |
Interfaces
6 interfaces between chains.
- B–C · 747 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 746 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 501 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 275 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 covalent (heme attachment, covalent ligand).
Compared structures
- 3QVZ · Crystal structure of the Zn-RIDC1 complex stabilized by BMOE crosslinks cocrystallized in… · the same entry in another collection · chain C against C, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3QVZ · PDBe 3QVZ
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