Research workbench
ATPase gspe in complex with the cytoplasmic domain of gspl from the vibrio vulnificus type II secretion system
Analyse ATPase gspe in complex with the cytoplasmic domain of gspl from the vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PHT
- Type
- protein
- Length
- 1,997 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein L; General secretory pathway protein E
- UniProt
- Q8DDT8, Q8DDT1
- Ligands
- ANP, ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Type II secretion system protein L | protein | 224 | 27% helix, 36% strand | Q8DDT8 |
| A | General secretory pathway protein E | protein | 438 | 40% helix, 27% strand | Q8DDT1 |
| Y, Z | Type II secretion system protein L | protein | 226 | 24% helix, 35% strand | Q8DDT8 |
| B | General secretory pathway protein E | protein | 442 | 40% helix, 25% strand | Q8DDT1 |
| C | General secretory pathway protein E | protein | 441 | 40% helix, 26% strand | Q8DDT1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains X, A, Y, B, Z, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.81 | 0.87 | 54 | empty |
| 2 | 442 | 0.78 | 0.86 | 59 | empty |
| 3 | 804 | 0.77 | 0.81 | 79 | ANP, MG |
| 4 | 414 | 0.77 | 0.86 | 51 | ANP, MG |
| 5 | 851 | 0.76 | 0.79 | 78 | ANP, MG |
Interfaces
7 interfaces between chains.
- X–A · 1754 Ų buried · 20 hydrogen bonds · protein-protein
- Z–C · 1708 Ų buried · 24 hydrogen bonds · protein-protein
- Y–B · 1706 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1000 Ų buried · 21 hydrogen bonds · protein-protein
- X–B · 325 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4PHT · ATPase GspE in complex with the cytoplasmic domain of GspL from the Vibrio vulnificus… · the same entry in another collection · chain X against X, 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 Q8DDT8
- Every structure of UniProt Q8DDT1
- Elsewhere: RCSB PDB 4PHT · PDBe 4PHT · UniProt Q8DDT8 · UniProt Q8DDT1
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