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Crystal structure of the C-terminal periplasmic domain of eceptc from escherichia COLI- complex with zn
Analyse Crystal structure of the C-terminal periplasmic domain of eceptc from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZZU
- Type
- protein
- Length
- 1,063 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoethanolamine transferase eptc
- EC
- 2.7.-.-
- UniProt
- P0CB39
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phosphoethanolamine transferase eptc (EC 2.7.-.-) | protein | 353 | 33% helix, 17% strand | P0CB39 |
| B | Phosphoethanolamine transferase eptc (EC 2.7.-.-) | protein | 357 | 32% helix, 17% strand | P0CB39 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.70 | 0.83 | 29 | empty |
| 2 | 442 | 0.64 | 0.78 | 34 | empty |
| 3 | 117 | 0.61 | 0.87 | 19 | empty |
| 4 | 58 | 0.52 | 0.87 | 19 | empty |
| 5 | 275 | 0.51 | 0.74 | 32 | empty |
Interfaces
2 interfaces between chains.
- B–C · 481 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 297 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 5ZZU · Crystal structure of the C-terminal periplasmic domain of EcEptC from Escherichia coli… · the same entry in another collection · chain A against A, TM-score 1.00
- P0CB39 · AlphaFold monomer V2.0 prediction for phosphoethanolamine transferase eptc (P0CB39) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0CB39
- Elsewhere: RCSB PDB 5ZZU · PDBe 5ZZU · UniProt P0CB39
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