MolNFT v1 · #76810 · protein
Crystal structure of the zn-RIDC1 complex stabilized by bmh crosslinks
3QW1 · Cytochrome CB562: “Crystal structure of the zn-RIDC1 complex stabilized by bmh crosslinks”. X-ray diffraction, 3 ligands (HEM, LCY, ZN), 8 pockets (best druggability 0.89). MolNFT v1 #76810 on GenesisL1: 3D structure, binding sites…
- PDB
- 3QW1
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome CB562
- Ligands
- HEM, LCY, ZN
- Pockets
- 8 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome CB562 | protein | 106 | 80% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- LCY · 1-methylpyrrolidine-2,5-dione · ligand · 4 copies · chains A, B, C, D
- 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.89 | 0.91 | 110 | empty |
| 2 | 137 | 0.59 | 0.83 | 22 | HEM |
| 3 | 124 | 0.58 | 0.84 | 21 | HEM |
| 4 | 157 | 0.57 | 0.81 | 22 | HEM |
| 5 | 142 | 0.56 | 0.81 | 22 | HEM |
Interfaces
6 interfaces between chains.
- A–D · 771 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 752 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 561 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 510 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 covalent (heme attachment, covalent ligand).
Compared structures
- 3QW1 · Crystal structure of the Zn-RIDC1 complex stabilized by BMH crosslinks · the same entry in another collection · chain A against A, 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 3QW1 · PDBe 3QW1
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