Research workbench
Structure of the periplasmic output domain of the legionella pneumophila lapd ortholog CDGS9 in complex with pseudomonas fluorescens lapg
Analyse Structure of the periplasmic output domain of the legionella pneumophila lapd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U65
- Type
- protein
- Length
- 886 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two component histidine kinase, ggdef domain PROTEIN/EAL domain protein; Putative cystine…
- UniProt
- Q5ZXA3, Q3KK32
- Ligands
- CA
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Two component histidine kinase, ggdef domain PROTEIN/EAL domain protein | protein | 131 | 50% helix, 27% strand | Q5ZXA3 |
| E, F | Putative cystine protease | protein | 181 | 47% helix, 18% strand | Q3KK32 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.73 | 0.78 | 89 | empty |
| 2 | 321 | 0.70 | 0.84 | 55 | empty |
| 3 | 483 | 0.62 | 0.75 | 52 | empty |
| 4 | 199 | 0.54 | 0.78 | 18 | empty |
| 5 | 168 | 0.48 | 0.76 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2016 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1994 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 736 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 681 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 671 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4U65 · Structure of the periplasmic output domain of the Legionella pneumophila LapD ortholog… · 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 Q5ZXA3
- Every structure of UniProt Q3KK32
- Elsewhere: RCSB PDB 4U65 · PDBe 4U65 · UniProt Q5ZXA3 · UniProt Q3KK32
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