Research workbench
The structure of kdgf from yersinia enterocolitica.
Analyse The structure of kdgf from yersinia enterocolitica. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FPX
- Type
- protein
- Length
- 228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectin degradation protein; Peptide
- UniProt
- A1JMF7
- Ligands
- NI
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectin degradation protein | protein | 106 | 3% helix, 58% strand | A1JMF7 |
| B | Pectin degradation protein | protein | 107 | 3% helix, 57% strand | A1JMF7 |
| E | Peptide | protein | 7 | 0% helix, 0% strand | — |
| F | Peptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–B · 1781 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 521 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 503 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5FPX · The structure of KdgF from Yersinia enterocolitica. · 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
- Every structure of UniProt A1JMF7
- Elsewhere: RCSB PDB 5FPX · PDBe 5FPX · UniProt A1JMF7
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