Research workbench
Crystal structure of zinc binding protein zint in complex with citrate from E. COLI
Analyse Crystal structure of zinc binding protein zint in complex with citrate from E.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YXC
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal-binding protein zint
- UniProt
- P76344
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metal-binding protein zint | protein | 187 | 29% helix, 30% strand | P76344 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.68 | 0.76 | 69 | CIT |
| 2 | 485 | 0.68 | 0.79 | 49 | ZN, CIT |
| 3 | 64 | 0.34 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 322 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YXC · Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
- P76344 · AlphaFold monomer V2.0 prediction for metal-binding protein zint (P76344) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P76344
- Elsewhere: RCSB PDB 5YXC · PDBe 5YXC · UniProt P76344
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