MolNFT v1 · #90192 · protein
Crystal structure of the S210C (dimer) mutant from the N-terminal domain of the secretin xcpq from pseudomonas aeruginosa
4EC5 · General secretion pathway protein D: “Crystal structure of the S210C (dimer) mutant from the N-terminal domain of the secretin xcpq from…”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.58). MolNFT v1 #90192 on…
- PDB
- 4EC5
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General secretion pathway protein D
- UniProt
- P35818
- Ligands
- CA
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General secretion pathway protein D | protein | 218 | 38% helix, 32% strand | P35818 |
| B | General secretion pathway protein D | protein | 208 | 38% helix, 32% strand | P35818 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.58 | 0.77 | 35 | empty |
| 2 | 98 | 0.44 | 0.79 | 14 | empty |
| 3 | 60 | 0.29 | 0.74 | 15 | empty |
| 4 | 52 | 0.28 | 0.75 | 15 | empty |
| 5 | 62 | 0.27 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4EC5 · Crystal structure of the S210C (dimer) mutant from the N-terminal domain of the secretin… · 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 0.36
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 4EC5 · PDBe 4EC5 · UniProt P35818
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