Research workbench
2.75 ångström crystal structure of hypothetical protein LMO2686 from listeria monocytogenes egd-E
Analyse 2.75 ångström crystal structure of hypothetical protein LMO2686 from listeria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K15
- Type
- protein
- Length
- 398 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO2686 protein
- UniProt
- Q8Y3Z3
- Ligands
- CL
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 67% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LMO2686 protein | protein | 138 | 0% helix, 62% strand | Q8Y3Z3 |
| B | LMO2686 protein | protein | 130 | 0% helix, 71% strand | Q8Y3Z3 |
| C | LMO2686 protein | protein | 130 | 0% helix, 67% strand | Q8Y3Z3 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.65 | 0.79 | 48 | empty |
| 2 | 354 | 0.59 | 0.76 | 41 | empty |
| 3 | 156 | 0.42 | 0.73 | 21 | empty |
| 4 | 84 | 0.30 | 0.73 | 17 | CL |
Interfaces
2 interfaces between chains.
- B–C · 1508 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1416 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 4K15 · 2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 from Listeria… · 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 Q8Y3Z3
- Elsewhere: RCSB PDB 4K15 · PDBe 4K15 · UniProt Q8Y3Z3
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