Research workbench
De novo designed two-domain di-ZN(II) and porphyrin-binding protein
Analyse De novo designed two-domain di-ZN(II) and porphyrin-binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JH6
- Type
- protein
- Length
- 696 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two-domain di-ZN(II) and porphyrin-binding protein
- Ligands
- 7BU, ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 91% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Two-domain di-ZN(II) and porphyrin-binding protein | protein | 174 | 91% helix, 0% strand | — |
Ligands and binding sites
- 7BU · [5,10,15,20-tetrakis(trifluoromethyl)porphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]zinc · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- 2PE · Nonaethylene glycol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.81 | 0.90 | 35 | 7BU |
| 2 | 370 | 0.80 | 0.90 | 35 | 7BU |
| 3 | 374 | 0.78 | 0.88 | 36 | 7BU |
| 4 | 443 | 0.78 | 0.86 | 49 | 7BU |
| 5 | 863 | 0.75 | 0.79 | 67 | empty |
Interfaces
5 interfaces between chains.
- A–C · 427 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 423 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 229 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7JH6 · De novo designed two-domain di-Zn(II) and porphyrin-binding protein · 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 7JH6 · PDBe 7JH6
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