MolNFT v1 · #141136 · protein
Crystal structure of zinc binding protein zint in complex with citrate from E. COLI
5YXC · Metal-binding protein zint: “Crystal structure of zinc binding protein zint in complex with citrate from E. COLI”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #141136 on GenesisL1: 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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