MolNFT v1 · #124179 · protein
Structure of designed zinc binding protein ZE2 bound to ZN2+
5K7J · Indole-3-glycerol phosphate synthase: “Structure of designed zinc binding protein ZE2 bound to ZN2+”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.82). MolNFT v1 #124179 on GenesisL1: 3D structure, binding sites…
- PDB
- 5K7J
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indole-3-glycerol phosphate synthase
- EC
- 4.1.1.48
- UniProt
- Q06121
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 240 | 42% helix, 16% strand | Q06121 |
| B | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 243 | 41% helix, 16% strand | Q06121 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.82 | 0.87 | 74 | empty |
| 2 | 306 | 0.72 | 0.85 | 40 | ZN |
| 3 | 52 | 0.45 | 0.84 | 18 | empty |
| 4 | 80 | 0.44 | 0.81 | 21 | empty |
| 5 | 60 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 433 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5K7J · Structure of designed zinc binding protein ZE2 bound to Zn2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q06121 · AlphaFold monomer V2.0 prediction for indole-3-glycerol phosphate synthase (Q06121) · a predicted model of the same protein · chain A 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 Q06121
- Elsewhere: RCSB PDB 5K7J · PDBe 5K7J · UniProt Q06121
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