MolNFT v1 · #90114 · protein
Crystal structure of the N-terminal domain of the secretin xcpq from pseudomonas aeruginosa
4E9J · General secretion pathway protein D: “Crystal structure of the N-terminal domain of the secretin xcpq from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.57). MolNFT v1 #90114 on GenesisL1…
- PDB
- 4E9J
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General secretion pathway protein D
- UniProt
- P35818
- Ligands
- MG
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General secretion pathway protein D | protein | 217 | 40% helix, 32% strand | P35818 |
| B | General secretion pathway protein D | protein | 208 | 39% helix, 32% strand | P35818 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.57 | 0.76 | 31 | empty |
| 2 | 94 | 0.46 | 0.80 | 20 | empty |
| 3 | 77 | 0.32 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 952 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4E9J · Crystal structure of the N-terminal domain of the secretin XcpQ from Pseudomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- P35818 · AlphaFold monomer V2.0 prediction for secretin xcpq (P35818) · a predicted model of the same protein · chain B against A, TM-score 0.37
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 P35818
- Elsewhere: RCSB PDB 4E9J · PDBe 4E9J · UniProt P35818
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