Research workbench
Crystal structure of the peptidoglycan binding domain of the outer membrane protein (ompa) from klebsiella pneumoniae with bound D- alanine
Analyse Crystal structure of the peptidoglycan binding domain of the outer membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RJJ
- Type
- protein
- Length
- 240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ompa family protein
- UniProt
- A0A422WJQ0
- Ligands
- DAL, CL
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ompa family protein | protein | 120 | 36% helix, 21% strand | A0A422WJQ0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.40 | 0.79 | 16 | empty |
| 2 | 76 | 0.35 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 941 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 7RJJ · Crystal Structure of the Peptidoglycan Binding Domain of the Outer Membrane Protein… · 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 A0A422WJQ0
- Elsewhere: RCSB PDB 7RJJ · PDBe 7RJJ · UniProt A0A422WJQ0
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