Research workbench
Fusion protein of T4 lysozyme and B4 domain of protein a from staphylococcal aureus with chemical cross-linker ey-cbs
Analyse Fusion protein of T4 lysozyme and B4 domain of protein a from staphylococcal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EWX
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENDOLYSIN,IMMUNOGLOBULIN G-binding protein A,ENDOLYSIN
- EC
- 3.2.1.17
- UniProt
- P00720, P38507
- Ligands
- EYC
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENDOLYSIN,IMMUNOGLOBULIN G-binding protein A,ENDOLYSIN (EC 3.2.1.17) | protein | 210 | 70% helix, 6% strand | P00720, P38507 |
| B | ENDOLYSIN,IMMUNOGLOBULIN G-binding protein A,ENDOLYSIN (EC 3.2.1.17) | protein | 214 | 67% helix, 6% strand | P00720, P38507 |
Ligands and binding sites
- EYC · 2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid} · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.46 | 0.75 | 18 | empty |
| 2 | 138 | 0.41 | 0.75 | 24 | empty |
| 3 | 130 | 0.37 | 0.73 | 21 | empty |
| 4 | 108 | 0.36 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 391 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5EWX · Fusion protein of T4 lysozyme and B4 domain of protein A from staphylococcal aureus with… · the same entry in another collection · chain A against A, TM-score 1.00
- P38507 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P38507) · a predicted model of the same protein · chain B against A, TM-score 0.34
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 P00720
- Every structure of UniProt P38507
- Elsewhere: RCSB PDB 5EWX · PDBe 5EWX · UniProt P00720 · UniProt P38507
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