MolNFT v1 · #107296 · protein
Structure of the periplasmic output domain of the legionella pneumophila lapd ortholog CDGS9 in complex with pseudomonas fluorescens lapg
4U65 · Two component histidine kinase, ggdef domain PROTEIN/EAL…: “Structure of the periplasmic output domain of the legionella pneumophila lapd ortholog CDGS9 in complex with…”. X-ray diffraction, 1 ligand (CA), 9 pockets (best…
- 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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