Research workbench
Crystal structure of low temperature requirement C protein from listeria monocytogenes
Analyse Crystal structure of low temperature requirement C protein from listeria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y9I
- Type
- protein
- Length
- 636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low temperature requirement C protein
- UniProt
- Q9ZIM5
- Ligands
- CA, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Low temperature requirement C protein | protein | 159 | 68% helix, 0% strand | Q9ZIM5 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.79 | 0.97 | 27 | empty |
| 2 | 275 | 0.60 | 0.79 | 28 | empty |
| 3 | 257 | 0.59 | 0.80 | 30 | CA |
| 4 | 318 | 0.59 | 0.77 | 38 | empty |
| 5 | 247 | 0.58 | 0.80 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1158 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1126 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1010 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1007 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 1Y9I · Crystal structure of low temperature requirement C protein from Listeria monocytogenes · 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 Q9ZIM5
- Elsewhere: RCSB PDB 1Y9I · PDBe 1Y9I · UniProt Q9ZIM5
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