Research workbench
Crystal structure of the NLEG5-1 effector (C200A) from escherichia COLI O157:H7 str. sakai
Analyse Crystal structure of the NLEG5-1 effector (C200A) from escherichia COLI O157:H7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VGC
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NLEG5-1 effector
- UniProt
- B6DZC0
- Ligands
- CA, CL
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NLEG5-1 effector | protein | 211 | 41% helix, 20% strand | B6DZC0 |
| B | NLEG5-1 effector | protein | 204 | 38% helix, 21% strand | B6DZC0 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.57 | 0.80 | 35 | CA |
| 2 | 76 | 0.38 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 989 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5VGC · Crystal structure of the NleG5-1 effector (C200A) from Escherichia coli O157:H7 str. Sakai · 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 B6DZC0
- Elsewhere: RCSB PDB 5VGC · PDBe 5VGC · UniProt B6DZC0
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