Research workbench
The crystal structure of a domain of a putative permease protein from porphyromonas gingivalis to 2A
Analyse The crystal structure of a domain of a putative permease protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IS6
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative permease protein, ABC transporter
- UniProt
- Q7MWD8
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative permease protein, ABC transporter | protein | 237 | 24% helix, 35% strand | Q7MWD8 |
| B | Putative permease protein, ABC transporter | protein | 217 | 25% helix, 34% strand | Q7MWD8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.71 | 0.77 | 81 | SO4 |
| 2 | 93 | 0.42 | 0.78 | 19 | empty |
| 3 | 87 | 0.40 | 0.77 | 21 | empty |
| 4 | 94 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 672 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3IS6 · The Crystal Structure of a domain of a putative Permease protein from Porphyromonas… · 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 Q7MWD8
- Elsewhere: RCSB PDB 3IS6 · PDBe 3IS6 · UniProt Q7MWD8
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