Research workbench
Crystal structure of a susd superfamily protein (BDI_3964) from parabacteroides distasonis atcc 8503 at 1.95 a resolution
Analyse Crystal structure of a susd superfamily protein (BDI_3964) from parabacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OTN
- Type
- protein
- Length
- 942 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Susd superfamily protein
- UniProt
- A6LIX4
- Ligands
- CL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Susd superfamily protein | protein | 471 | 47% helix, 9% strand | A6LIX4 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
- ACT · Acetate ion · additive · 11 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.86 | 0.90 | 64 | CL, ACT, EDO |
| 2 | 287 | 0.76 | 0.89 | 49 | PEG, EDO |
| 3 | 247 | 0.75 | 0.89 | 36 | empty |
| 4 | 62 | 0.56 | 0.88 | 12 | EDO |
| 5 | 87 | 0.52 | 0.84 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 1415 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3OTN · Crystal structure of a SusD superfamily protein (BDI_3964) from Parabacteroides… · 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 A6LIX4
- Elsewhere: RCSB PDB 3OTN · PDBe 3OTN · UniProt A6LIX4
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